Sorry to jump in, but I've been following the last couple of pages. On a certain level, I can see your point, Cirno; if a wizard has access to most or every spell in the book, and he has the time to prep every or at least most encounters, it could be very difficult to frustrate him. With those resources, he can literally write a new ending to the story.
Thing is, speaking as a wizard player, you don't and shouldn't have access to those things all the time. Your murder mystery example only works if the mage has the spell. A DM can keep scrolls and wands away from the wizard for that adventure; if that magic were that plentiful, there wouldn't be a mystery in the first place. Besides that fact, the deceased doesn't necessarily know the answer
Your other examples have similar issues. The lower-level spells you mention are not terribly unbalancing except in the most rudimentary setups. The knock spell can unlock most doors, but it doesn't disarm traps (which there is no spell for). Arcane Lock locks most doors, but the lock doesn't matter if the door is bashed in by a fighter, or the lock dispelled.
Fly is only a pain if you are trying to lock them in a hole. Archers can make short work of a wizard scout trying to do recon. Traps or odd setups cure its use in any locked rooms with ledges.
Summon Monster is not terribly bad. At lower levels, who really cares about badgers, and at upper levels banishment/antimagic is a real pain.
Polymorph is a pain in the rear, but size and level constraints are sort of put a muzzle on it.
Time Stop isn't really a problem. A character can't do a whole lot, and the level/benefit causes most people to overlook it during spell selection.
Invisibility gets canceled/thwarted by so many things that a single failed role can leave worse off then if you hadn't tried to sneak by magically at all.
Blur and Mirror Image do give cover bonuses, but in the case of Blur it's much better to be used on the fighters then the wizard. Mirror Image is a pain, but area effects counter it nicely and can take the wizard out of the game entirely.
Disintegrate is the worst one, but even it is muted. It can only disintegrate 10x10x10 of matter, so a small hut or large rock. Normal weapons and shields are of course dead. An average amount of damage is 100 for that spell, which is a lot. A high fort save by the target limits its likely damage to 15 points, which isn't that much. It's actually less then the average fighter of equivalent level.
Clerics are worse then wizards because they get total access to their spell lists without any kind of control built in. Plus armor.
The point of all this has not been to poke holes in the handful of examples post here; rather, just to illustrate two things. First, that it isn't as all powerful as it seems, second, that the wizard may be able to rip reality, but the DM gets to line it with kevlar.
If a person wants to play a game like a Conan novel, where the mage is limited to colorspray and divination and the entire plot hinges on the fighter making that natural twenty to throw his sword across throne room and hit a tiny gem stone, then I completely agree with you that the classes as written do not fit in that fantasy world. <For clarity, let me say that the tongue in cheek tone of the above is me ragging on the Conan films/comics, not your position or anyone elses>.
If you have a world where arcane magic is rare, and your adventures are prepared that way, then I concur the wizard class is unbalancing.
If a person wants to play in the traditional D&D world where the clerics augment the fighters into blessed juggernauts wading into undead foes while the wizard spends several rounds trying to send them back to the graves which the party rogue is currently looting, then they jive quite nicely in my experience. Just my 2 cents though.