wow beautiful and well written post arrowhawk! :O in the end you did clarify everything, going to the very concept of it. it makes no sense 'balance' a roleplaying game, it is not a math game, it is not a chess game, it's not something that can be defined with pure mathematics. a roleplaying game is basically another world and, reality.. isn't balanced, at all (so aren't my campaigns either the heroes doens't always win, at all.). mages? well they are scary, a well prepared mage can do virtually everything, and the only protection against them is.. more magic, whathever is in form of magic items, or another mage, or a cleric, or.. smarts!
you know that detect invisibility doesn't find people hidden in shadows? and also true seeing can't pierce trought a nonmagical disguise?... if I slap on my face a pair of fake mustaches... hey it's there, it's real, it's not an illusion, and a thunderstone can DEAFEN?.. (deaf! now you got 50% of failing a spell requiring verbal components..), a blinded mage for example cannot target people with spells..
in the end, it's all a matter of.. brains! (mmm brains..says the homer-illithid) if you know your enemy you can fight him effectively, mages and clerics are a reality in D&D world, no need of balancing, you just need to, bother with considering them in the big picture and tailor situation keeping them in count..
also with npcs! they themselves doesn't have limitless resources, if they kidnap a baron's daughter they wil keep in count that the baron might hire someone to rescue her, they surely know how much money the baron has (else why kidnapping the daugher?) and more or less can understand what kind of theat they can be put against.. again use smarts, why keep an hideout, if they can wander tru an intricate forest they know well.. a mage scries upon them, oh wow they are in an intricate forest I don't know, I study well the area for a teleport! oh wait! darn they are moving! and.. KEEP on moving, how the hell I teleport to them? plus the forest looks all the same to me...
they can set traps in the forest they know, keep on moving, and have a dozen of small hideouts while other of them whych remains in the baron castle spies upon the baron and keeps on 'communicating' terms of pay them the randsom via anonimous letters.
it's a dangerous game, but fun!