Keep ability scores as 3-18. I know some people want to make it just the mods, but I don't want to go that way.
Keep classes/levels. First off, these are pretty much the defining feature of D&D. Without them, you're definitely playing something else. I do think the concept could be refined a bit, though. I'd like to see them made into broad, but discernable, fantasy archetypes: Heavy fighter, light fighter, priest, studied arcanist, naturally gifted caster, etc. PrCs should reflect specific applications within an archetype, and multiclassing should be set up in such a way as to allow the blending of archetypes. Feats are for fine-tuning and customizing.
For ranger, go more toward 1E. A tough borderlander who uses whatever tools are at his disposal (including spells). TWF is just plain stupid as a core ability. And scout is completely the wrong way for the ranger to be going. My preferrence would be to hybridize the 3E ranger and the 3E barbarian, taking some of the features of each, but losing enough to be balanced. One of my biggest WTFs is the d8 hit die. Anyone who thinks that goes with ranger isn't even discussing the same concept as me -- or with prior editions, IMO.
Paladin as a base class, though, is a sacred cow that needs steak sauce. It's pretty much a poster child for what a PrC should be.
I'm torn on Vancian magic. On the one hand, the system sucks, strains suspension of disbelief, and runs counter to most fantasy fiction. On the other, it's been then from the start. Personally, I'd like to see it move toward a non-slot-based system (points is fine, I guess) and have scalable spells, like XPH.