How to Handle Clerics (and other troubling shortcuts).

So as I GM higher and higher level games I discover certain things about how disappointing certain

Iconic Pathfinder Cleric - not bad.

abilities can be.  Specifically there are certain spells and abilities that ruin some of the best things in D&D: traps, tricks, doublecrosses and undead monsters.  Many of these abilities are lodged in the cleric, this isn't the cleric's fault - it seems reasonable that clerics have these abilities, but they still tend to make things less fun. Player's sometimes don't realize it's not fun to not have to think, or realize that spotting and avoiding traps is more rewarding if it's a product of actual player skill - but it's true.  Ok that's not fair, players want to survive without too much trouble and many support spells allow this, it's the GM's job to deal with these spells in a way that's interesting. Below are several ways I propose dealing with certain abilities that players have.  I don't think these are improper GM behavior, railroading or GM fiat and I don't suggest removing player abilities, only means of limiting or interpreting them it to keep challenge in place.  It's also worth keeping in mind that powerful opponents and dangerous places in worlds where miraculous spells exist may have their own divine protectors or other means of dealing with the interventions a Cleric or mage can call up.

General Thoughts: Most of the abilities of the Cleric (or magic-user - which is almost as bad) are single use spells.  The obvious way around this is to make sessions longer, so that the party faces an increased number of challenges and need to burn spells.  Yet most games I'm involved in are 2-3 hours maximum and spells conservation (especially when there are several casters as their always seem to be) is less of an issue. A similar option to long games is to pile stuff on, more traps, more tricks, more invisible monsters, or combinations like invisible traps.  This is the classic Gygax method, but I along with many other players of tabletop RPGs hate the sort of heavily protected adventure where every wall cannot be bypassed, every NPC has a slew of magical protections from charms and mind reading and divination and such.

The solutions I propose I think fit better with my game.  The key to keeping Clerical abilities interesting is remembering that while the deities wish to aid their servants, the gods are also distant, inhuman and easily annoyed.  As such a cleric who doesn't use her magic in the way that her chosen deity wants is likely not to get it. No god wants to be involved in a continual light flashlight assembly line, or to be constantly be used as a trap detector/predictor of what's around the next corner. Additionally even when the deities want to help they aren't always good at providing it.  What's a trap or dangerous to a divine being with strong moral opinions may be different then what's dangerous to an adventurer, and I can see a casting a detect traps spell finding things that present danger's to a cleric's purity or religious well-being while missing stuff such as precariously balanced boulders.

Turning: Turning the undead is fine, turning undead automatically and annihilating everything undead is dull.  Since this is the function of the cleric I don't want to come down hard on turning, but it can certainly make undead challenges less exciting for a party with a strong cleric or several clerics.  Yet the classic answer of gimping clerical ability (so very popular in early modules) is equally dull.  I don't think tossing out -2's to turning rolls for every gang of undead that the GM wants the party to fight is much of an answer.  Let the Cleric demonstrate thier power, turning skeletons to ash and driving off wailing spirits.  The party may have a hard fight, but the other players should realize that without their cleric it'd have gone much much worse. Still, it's not just number that can make turning less overwhelming, recognizing that turning is a limited effect that harms only a certain number of targets and that undead aren't all mindless attackers goes a long way towards solving the issue.

In Game Fixes: First, not all clerics turn undead.  It just doesn't make that much sense that every empowered religious figure would have dominion over the undead, sure the walking dead an an abomination, but some deities have axes to grind with other things, and their Clerics should reflect this.  Nature deities may turn aggressive animals, elemental deities turn elemental foes and I can even envision a god of thieves whose priests can drive off the forces of law (or at least make them ignore the god's servants).  Of the HMS Apollyon's three indigenous churches only one turns undead.  The Ship Spirits can instead drive off creatures of decay such as fungus monsters, demons and rogue automatons, while The Church of the Leviathan empowers it's clerics with the ability to turn devils and control sea creatures.
Most import though is to remember what turning does, it simply drives creatures off, holding them at bay.  Trying to capitalize on this effect and destroy the retreating undead is likely to make them aggressive again.  Intelligent undead are should have a chance to fight off the effect of turning if they have to, and should get a saving throw after if the turning persists for too long. Even reanimated bones and other simple creatures are likely to flail out at melee attackers while turned and even a skeleton should be allowed to counter attack if attacked while under the effect of turning.  Secondly it's important to think of turning as having a range.  The undead are likely only to retreat outside of that range - perhaps for dramatic effect this is the radius of light around the cleric, so the zombies will wait patiently beyond torch range for the turning effect to stop.
Additionally, undead aren't all dumb. While mindless undead might be herded into a pit or up against a wall where they can be smashed at range, even semi-intelligent monsters are going to try to negate turning's effects. Ghouls will throw rocks and bones from the shadows and run off if they can't do any damage, while wraiths and other immaterial creatures will likely hide or flee to return to their haunts once a Cleric is gone.  This becomes a greater problem when a wraith returns to find its crypt despoiled and treasures gone.  Intelligent undead like vampires or ghosts are even more likely to have ways around turning - perhaps they themselves have deities and can turn the servants of the gods of the living, perhaps they will send a wave of thralls or lesser undead to hold the clerics attention and perhaps they will simply retreat and bide their time - undead of course have an abundance of patience and time.  It is also equally certain that intelligent undead will both guard their lairs with unholy glyphs and similar protections from good, and that they will single out clerics for any surprise attacks or hit and run attacks.
Finally, lesser undead are still dangerous at high levels, not individually, but because they roam in huge numbers.  A party with a 6th level cleric should be able to handle 200 skeletons, or at least not be surprised to face them.  Why wouldn't a lich or necromancer have amassed armies of this size, and use it mercilessly to stop intruders.  The cleric may be able to account for 2D6 skeletons a round, but that's not enough to stop a huge swarm.

Continual Light: Quite possibly the lamest spell.  Continual Light isn't horrible because of what it does, it's horrible because how it does it and the feel it provides to the game. Every player thinks they are incredibly cunning to have a pouch full of small stones with continual light cast on them, or a headlamp, or some other contraption that makes the use of magical light into a boring gadget that one could find at the adventurer's version of REI. It's this cheapening of magic that annoys me mostly as an aesthetic matter. Sure I can see it being fine if one played in some sort of high magic setting, but I like my magic creepy and wondrous.
There's not really anything wrong with a mid-level party having access to steady light sources without tallying torches and lamps.  The problem as a technical matter is that a satchel of continual light rocks makes magical darkness trivial.  Magical darkness is a powerful effect, and creatures of the underworld should use it more.  Getting rid of it should also take some effort and the use of a light spell.  Stockpiles of continual light objects make darkness useless.  One solution is to have those casters of darkness carry around a satchel of continuous darkness objects, making a contested area flash like a strobe light until one side's satchel of light effects is gone.  This is terrible.

In Game Fix:  (Stolen from Brendan at Necropraxis) - Continual light, unlike light, cannot be cast on individual objects, it's an area effect.  One casts it in a room or location and it stays their, filling the air with divine or mystical illumination. It also either slowly decays without elaborate and costly rituals, or an individual caster may not maintain more than one continual light at a time.  This makes the spell useful for setting up protected areas within a dungeon or preparing a battlefield, with constant magical light to keep the underworld at bay, but prevents it from becoming a mundane fix for any vision related difficulty.

Find Traps: A spell that usually makes thieves feel fairly useless, and can be frustrating.  Clerics develop the ability to detect traps at third level, and while many will opt for Hold Person to improve their effectiveness in combat, Find Traps is also extremely popular.  Now I can see the value and use of Find Traps in a classic old school dungeon crawl, where traps are everywhere, deadly and well concealed. Personally I don't run my games this way, as my dungeons are not funhouses where installing a moving wall, animated statute or explosive runes is a regular weekend activity for the residents.  When traps are themselves puzzles, rather than simple skill checks, find traps becomes both irksome and at the same time easier to deal with.  Find Traps has a very minimal description, but many players seem to think that it allows the Cleric to discover and also figure out how traps work. I don't agree, I think Find Traps is best approached as an imprecise means of divine intervention to detect danger.

In Game Fix: The simplest way to amend Find Traps is to reduce it's duration to the two turns described in OD&D.  Two turns rarely allows the examination of many rooms, but with the fifty minutes found in later editions, parties often try to scout an area and then have a cleric dash about looking at everything that is trapped. In either case remembering that Find Traps has a duration and takes time to work (Cleric must stand in place and let the divine presence radiate outward searching for danger perhaps - basically it takes a turn to do a room.) if important.  However, I don't think reducing the time on the spell is necessary, four or five rooms is fine, because like all Clerical spells it's important to consider how the deity will interpret a petition.
What does the divine consider a trap?  What does a god consider dangerous to its followers?  Simple mechanical and magical traps, like spear trap or explosive runes, are undoubtedly detected, but one must wonder what else is.  I don't allow find traps to detect environmental hazards or items that are incidentally dangerous.  For example, a pool of toxic sludge is not a trap, nor is a weak floor, a roaming green slime or a cursed altar.
Additionally, just because players realize something is trapped doesn't make it easy to deal with.  Good traps often announce themselves anyway. Prying the gemstone eyes out of the Orcus statute, a series of holes in the walls, a silver grid inset in the floor? Is Find Traps really necessary to realize these are likely traps?  What the party needs is to think of a way to bypass these traps or to ignore them and move on.  This is really the key with traps, they are puzzles to figure out - not simple gotchas for failing a dice roll or not saying the magic words "we search for traps" every time a new room is entered.

Augury/Commune:  Potentially total game killers.  Along with Find Object and spells or objects that allow mind reading these things ruin any kind of mystery or treasure hunt if they are used in a cavalier manner.  The real problem though is that Commune and Augury create railroads.  A player gets to basically ask the GM "What should the party do?" This is boring and should be antithetical to the spirit of open world exploration so beloved in the OSR.  The issue then is really how to separate GM knowledge for in-game deity knowledge.

In Game Fix: When dealing with these spells it is key to remember that these are the result of the Cleric speak directly to their deity.  Because of this an augury of commune shouldn't be some sort of simple "is the door safe" kind of question.  Deities are petulant at the best of times, and presumably interrupting their ambrosia and nectar time for petty questions about dungeon layout and where the treasure is hidden will really annoy them.
A second issue if that deities aren't all seeing and all knowing in my games, and really in the sorts of polytheism that most games embrace they shouldn't be.  Each deity has a narrow set of goals and interests and anything outside of that is likely to be of little interest so an commune spell will get some kind of general platitude or vague answer that conceals the extent of what the god doesn't know. For requests that involve a need to know things that are sacred or dangerous to the worshipers of other gods, the cleric's deity's indifference may not be the only obstacle, a rival god may actively interfere, preventing the clerics deity from knowing things or making learning them hard for the deity to do without risk and effort.
Finally deities may not see things in a way that's helpful to players, and in myth and legend always enjoy giving incomprehensible riddles rather then straight answers to questions. It seems perfectly reasonable that a god would only communicate through omens and portents that the cleric will still need to figure out.  All these tactics can be combined to make spells like commune and augury goads to player action and puzzles to be solved rather than road maps, railroads or solutions.  It may take a little effort to determine what the deity will say, but when dealing with a party that can cast divination spell it's worth putting a little time into figuring out what information a god will provide and how they will provide it.