I have played several Pokemon games (currently playing Black), and I've always ended up with the same problem: lagging behind on my Pokemon's levels because I'm training were more Pokemon than the game expects me to. Absolutely unable to choose 6, I usually limit myself to 10 active Pokemon plus 2 or 3 utility Pokemon (for Cut, Flash, etc.), but that means I always end up having to fight wild Pokemon to level up my large team, and also using the PC a lot, which is not available at all locations.
On the plus side, when I challenge a gym, I can choose the 6 Pokemon that have the best type matches for the Pokemon in that gym. It's harder to choose for the Elite 4, but it's still good to have a choice. Still... leveling up so many Pokemon is an annoying task.
Have you had any similar experiences? How many Pokemon do you usually train? How do you choose which ones to train and which ones to leave behind?