I absolutely, positively prefer skill based sandbox-esque character development to class specific skill sets, bugs, imbalances, problems and all. It's the most exciting aspect of CRPG design in my opinion, and makes for more interesting, emergent gameplay styles and character builds. Even if 99% of the time the game surrounding such these skill systems cannot accommodate the wide scope of builds, and is thus easy to break.
For this reason Arcanum has, without a doubt, my favourite character sheet ever, and even with it's imbalanced and arguably broken game world, it's the game I feel best captures the general philosophy of CRPG design. At least, in terms of granting players a near unlimited scope of skill/ability combinations, and so allowing them to truly 'role play' as anyone they wish, in a world that allows them to do such.
I also think that aside from the more broken stretches of gameplay (hello mines), Arcanum is littered with phenomenal quest/world design that accounts for an massive variety of play styles and builds.
I'm not down on class based skill trees, and can see the logic of such things in party based games. And, to be honest, this direction always leads to more polished, tactical and better 'playing' combat systems for RPGs. But I'll be damned if I'm not much more enthralled and fascinated by full skill trees.
EDIT: The above fireball Mage / herbology example is exactly why I like skills versus class. It doesn't matter how 'realistic' or what argument can be made for characters/classes behaving a particular way because the developers want them to. The skill system simply says that if you can make something work, if you want to make it possible, you can do so. Just like the real world, even if it leads to difficulties down the road. If you absolutely want to study fireball casting and herbology, you can, because there's no real reason you shouldn't be able to except for arbitrary design restrictions.