I think it comes down to you preferring a control scheme that uses fewer buttons, and achieves special functions through combinations of buttons, whereas the trend is using more buttons and a dedicated one per function, when possible.
The problem is that too many developers see all the buttons on a controller and feel that they have to use them all, even if doing so makes the game more complicated. Like one button to draw a weapon, another button to ready/aim the weapon, another button to fire the weapon, another button to reload the weapon, etc. Did anyone actually complain back in the days when you just pressed one button to make your character draw a weapon and fire it, reloading automatically as needed? Did people say "This game would be better if I had to use more buttons to accomplish the same thing."?
There are a lot of PlayStation 1 games with control schemes like that. Colony Wars is a series that annoyed the crap out of me with inverted flying controls. Only the last title in the series had an option for a better control scheme.
I kinda get why they did that back in the day - you fly a spaceship so they went with standard aircraft controls. Nowadays, it's very hard getting used to these, though.
And yet nobody has designed a real plane with non-inverted controls.
The part I find strange is that forward=down, back=up is how pretty much everything in the real world capable of tilting works. Put your hand on top of your head and look down. Which way did your hand move? If you have a camera on a tripod and you put your hand on top of it, do you pull back to make it tilt down? If you were behind a mounted machine gun and wanted to tilt it down, would you push down on the back end of it? So why would you move a mouse/analog stick back to look/fly down in a game?
As for controls I hate...
Postal - It looks like an action game, but it uses the control scheme of a first person shooter. In theory this gives you gives you great flexibility in how you move. In practice, it sucks because unlike an FPS game, the camera is always fixed at the same angle. It is NOT intuitive to push left to make your character move right if they're facing the screen. Or if they're facing right, then pushing left will make them go up, and pushing right will make them go down. I'd rather the game just control like a typical arcade game.
Resident Evil/Dino Crisis/Alone in the Dark/others - Stupid tank controls.
Auto-aiming in DOS games - I want to shoot the explosive barrel, not the enemy standing next to it! Stop hitting the damn wall and throw the dynamite into the doorway where I'm aiming!! STOP SHOOTING THE %$&#@! ANIMALS AND TARGET THE ENEMY I'M AIMING AT!!! ARGH!!!!!!!!!!!!!!!!!!!!
FPS games on consoles - Aiming with an analog stick sucks. Every console since the PS2 on has had USB ports, so why don't these games support mouse and keyboard?