Great suggestions. Agreed with most of them esp. the idea of active combat. Had to disagree with the sub based model though.
Anyway, not sure if it's already out there, but one thing I'd like to suggest would be learning skills dynamically (not sure if that's the correct word for it..)
Actually there are 2 different variations for this idea, and I think it would work best with having no classes just like what you've mentioned.
1) Partially hidden skills & skill trees
What this means is exactly what it is. Everyone would have a basic skill tree with only basic skills.
What do I mean by basic skills?
Skills like 'Slash', 'Block', 'Charged Shot', 'Fireball', 'Heal'. So all you have at the start are basic skills like these.
Grinding and chaining these skills together or even with a movement would unlock advanced skills, which are hidden from the skill tree itself. This would reveal paths for the current skill tree, and could even lead to revealing new skill trees.
A player grinds basic skill 'Slash', and the skill reaches level 5. He'd unlock 'Power Slash', originally hidden from the basic skill tree he had at start. Later on, he found out that it was cool to use 'Power Slash' with a jump. After doing that for quite some time, he'd unlock 'Ground Slam'. These skills would still be under the same, basic skill tree, but they'd be more on the close combat type of skills. So, unlocking more close combat skills by just grinding, chaining of skills, and maybe even luck, he'd unlock more close combat skills such that it reveals a path on the skill tree that lets him focus on close combat skills if he wanted to, by showing ways on how to unlock those skills (mostly through grinding+chaining), and eventually he'd be able to unlock a totally new skill tree, to 'master' close combat skills
2) Fully hidden skills & skill trees
Similar to the idea above, except that everyone would start with no skills at all. They'd have to learn them either from the experience and luck like what I've mentioned above, or, from scrolls, tomes, etc. (esp. mages)
E.g. repeatedly using normal attack with a sword unlocks basic swordsman skill tree, with a basic skill 'Slash' and reveals other basic swordsman skills in that tree, and how to unlock them (again, like what I've mentioned above, mostly through grinding+chaining)
Well, that's it for my suggestion. A bit long though. :l