FO3s skill system issues are

a) lots of useless skills (most skill based systems have this problem)
b) you'll probably max out most skills in a playthrough (pretty much in the vein of the TES games)

It was harder to be a jack of all trades in the earlier Fallouts.

Obviously class based systems are easier to balance and implement, but I feel that actually building up your character tends to be less interesting in such games if the development is too railroaded. And a class based system that allows a lot of customisation (for instance 3rd edition AD&D which I like) wont play all that differently compared to a skill based system.