Hell yes.
The only time I slum it with a stock controller is when I'm eating and playing games at the same time. I don't want potato chip grease on my $150 controller.
You make a great point about the brain not cooperating though. You have to muscle through it until it becomes second nature. The way I think about it is that there is no doubt that it's better to use the bumpers if (a) it means you don't have to move off the control stick or another button; and (b) it doesn't interfere with the gameplay. Sometimes there is a fine line. Example: In the games where you run by pushing in a thumbstick, I found that, initially, I would inadvertently click a bumper button while running. After a while that tendency went away with better finger placement. Anyway, if you realize that you're better off with them, but you're just not used to them, resist the urge to stop using them. You'll get it. Heck, I go back to Atari 2600--one button!
Having said all that, even if you remove the bumpers and use the stock thumbsticks, the controller is still worth $150. I promise.