I couldn't agree more.
The problem is that in D&D, especially in 3.X, Magic sits right on that pedestal. Using an axe to solve problems like a locked door by its nature has consequences. Magic doesn't. It's an almost consequence free "I win" button handed out to the spellcasters. And it can be used in almost any situation. Diplomacy? Sure. Lockpicking? Great. Travel? Great. What can't it do.
What is the downside to using Knock? You have one fewer "I win" tokens to use on subsequent doors. You don't even have to roll.
Take magic off that pedestal. Either make it less powerful at picking locks than skill at lockpicking, or give every spell a chance to blow up in the caster's face. Or sharply limit it either through actually having limits like Vance (no more than half a dozen spells prepared at one time and substantial time to reprepare) or through rules (e.g. all magic is illusions, or all magic is elemental, or...)
Every other thing you can do has places to apply it and places not to. Magic is the universal solution.
I think you're getting a bit overblown here. Magic is not an automatic "I win" button, nor is it consequence free, it simply has a different set of consequeces than other solutions.
Locked Door:
Solution - Consequence
Lockpick - Skill check, expose to trap/mimic/ear seekers
Key - none
Magic - Spell slot, Can set off trap or wards or magic detector
Axe - Time, loud, might set off trap, might make mimic crap itself
Bribe the doorman - Cost, time, might be betrayed
That spell slot is not a negligable cost. A wizard has got, at best, 5 spell slots for 2nd level spells. Is he going to fill those with knocks? Why? Isn't freeing those slots up why he brought the [-]hobbit burglar[/-] rogue along in the first place? A rogue can make lockpick checks all day long with no risks besides the occasional trap and he has skills to detect those traps, unlike the wizard who needs to spend
another spell slot to do that, for a few minutes. A Sorcerer is even worse, he gets to know 5 2nd level spells
ever. If he spent one on knock he should get to open a door or two with it.
Oh wait, someone could just buy a wand of knock! Then they don't need to worry about opening the next 50 doors!
I should bloody well hope so! 4,500 gp, let's see what else
we might get with that money. About a half-share in a longship or caravel. A trip to America for the entire party. A hireling wizard to cast the spell 75 times. Or a thousand skilled workmen for 2 solid weeks, enough time to excavate the entire dungeon from the top down like an archelogical dig!
The cost of a knock spell is only trivial at high levels, and at high levels any door short of the gates of hell
should be trivial. At that point the fighter has adamantine weapons and the wizard has disintegrate. Doors are not a problem anymore, it's what's behind them that worries you.
Nor is magic universally applicable in 3e, 3e was rife with anti-magic zones which shut wizards down completely. A rogue never has to put up with anything like that.
As far as 5e goes, I personally would like to see wizards have only a handful of vancian spells per day. Something like level or levelX2 spell levels worth, plus I want to see most 'utility' magic moved into the ritual magic space innovated by 4e.