Because slowly improving your character till he is near perfect in some areas, is a long honed tradition to achieve player satisfaction in rpgs. I think mainly because it makes it more your character and not like Sam Fisher some superhero typ everyone else got too.
Like the absurd health system, the unrealistic huds and several other aspect games tend to have, it's not necessarily realistic or everyones favourite thing, but it's established and accepted.
For the gameplay well you could argue, that slowly getting from bad and limited to very good helps to use your skills better, because they arn't that reliable at the beginning so you have to think more how to even the odds and it eases the learning curve slightly by slowly introducing new talents and abilites on top of the starting ones instead of dropping you into a pool of over the top talents.
On a personal note, I'm especially glad they did it this way, because Splinter Cell always felt to easy. The combination of an absurd amount of "stealth" and quite extraordinary aiming, made the games way to easy for me. Sure I may have been a superagent, but I was mainly a rather bored one, because the challenge was near to nonexistent. Something I felt Alpha Protocol only became near the end with maxed abilites, especially due to shadow operator.