what about a system where each kerbal learns their dicipline by doing things that actually have something to do with their dicipline. kerbals that have the flag pilot, can learn all the other skills, but piloting a craft is something that he is just better at. All the way up to level five with the skills named by pthigrivi, however, by doing things from another dicipline, like making crew reports, or repacking parachutes and things like that, with a lot of practise, this pilot can learn it to be a scientist, and an engineer. I also think it would be fair if an engineer would gain less experience points from flying mission than a pilot, however, a second try will gain gain him also some exp. (of course his doesn't happen with the pilot, he learned it the first time, so there's nothing new for him).