Just a few things that I hope to see covered in Pathfinder eventually, mostly my own current nitpicks with 3.X. Leaving out the things I already see in the works for changes (like skill consolidation (very good), and giving classes more to do), here is a short list of things I look forward to seeing your take on!
Prestige Classes: I hate the current glut of them. They stopped feeling special almost immediately (part of that I know is a GM thing, you have to control what comes into the game and how easily it is gotten by PCs). Personally I would love to see Prestige Classes all be 5 levels and just ooze awesome at each level. Make them something special, not just a better base class. On a similar note however, the base, core, classes should be viable and interesting all the way to 20 (or epic levels). Looks like you have made a great start on that however so far!
Skill DCs in combat: Only way I can think to list this one. Stuff like Concentration checks and the like are WAY too easy currently. I think the introduction of the CMB you have in the first alpha release is good though, and could be easily applied to things like Concentration checks and the like, so that they remain a challenge and not just a speed bump of sorts once you get past a certain level.
Magic overshadowing Melee: Another minor peeve, which you seem to be addressing already, is how, once you get into the mid teens or higher, magic trumps melee too easily. Fighters and the like should be able to do cool stuff and contribute to the group. The stuff I have seen so far is a nice start and I hope to see that trend continue!
One Core Book: Mostly meaning the players rules here. Hopefully once you make the final release of Pathfinder, it will be in the vein of Arcana Evolved, where I only need it and don't even need to crack open my 3.X PHB unless I happen to want something unique out of it. I am a much happier gamer when I can carry around only a couple of books or so, instead of needing a small rucksack to carry to each game. :) Of course, since I moved recently and most of my gaming is now done via virtual tabletop/voice chat, that is less an issue. But it is still nice to only need to reference one book!
Magic Item Bloat: This is one I really hate. I always felt that magic items should be kinda unique and special. As it stands now, they are practically required, to the point of PCs needing magic item shops and walking around with enough magical gear to glow in the dark and read by! :) It would be nice to see a way to reduce that reliance on magical gear while not making PCs weaker, thus making actual magic items special again. That is kinda a hard one to do though, but definitely something I will be watching for! One way we handled it in a low magic game was giving PCs something every couple levels (like stat increases, but it could apply to other things. Our DM had a nice chart worked up, and it pretty much replaced bog standard magical gear like +1 rings and such, so that the actual magic items we found DID things, rather than just added to our stats, since that was not as needed).
Anyways, looking forward to seeing more on this, what I have seen so far has actually gotten me excited about DnD again, so I am chomping at the bit to see/test more!