You forgot the other choice. The hybrid. 3.X is a hybrid as is Warhammer Fantasy Roleplaying (well 1e and 2e). They are systems that can be played as a class system, or a system where classes are really just skill packages bundled together.
In the idea of simply skill packages I definately dislike a system like 3.X as it's typically not really that fun if you have a power gamer, munchkin, or other such individual set upon getting their fun at the expense of everyone else's enjoyment.
However, I really enjoy Warhammer RPG (1e or 2e) as that type of classed skill packaged system (where classes really aren't that significant other than getting some sort of skill or ability that you desire).
Other classless systems, while amusing, sometimes aren't my cup of tea to play all the time (Amber RPG for example...not quite my flavor).
On the otherhand, if using the hybrid gamesystems as Classed systems, rather than as skill packages that are called classes, I actually enjoy the 3.X system more than the Warhammer system in that light.
So it depends.
On the whole however, I'd say I like the Archtype Class systems best, where you have a class that you can tweak slightly...but it's the roleplaying that really is the difference (1e...now that's more my style).