I'd unify mechanics more.
Combat maneuvers were a huge step in the right direction, but with ACG they diversified them in a bad way, making it too big an investment in feats to stay good at them. And there are subsystems, like feint, that could be part of the combat maneuver rules.
For some reason, saving throws have half the spread of most other things in Pathfinder. BAB ranges from 1-20, skills from +0 to +23, saving throws have a spread of 2-12 for no real apparent reason (attribute modifiers taken out of the calculation).
The skill rules could use 2-3 times the page count they got in Pathfinder. I don't want more skills, I want more rules for how the existing skills work, especially at higher levels. A lot of the perceived superiority of casters in Pathfinder is becasue of the skill rules are weak, IMO. Pathfinder skills feel lacking next to 3.5, and things like Stealth and finding traps are almost back in 1E land - the rules are so lacking that you HAVE to have house rules/interpretations.
Then there are a some small niggling bugs that crop up - like the rule that human rogues cannot sneak attack when in dim light. Rogues, stay out of the dark alleys and in the bright light of high street!
Otherwise, I don't see a lot of revision room in Pathfinder - it runns fairly smoothly and has about as many options as a class system can have. Adding more options through archetypes is nice, but ultimately runns into a grey wall of lost class distinctions.
1) Make it faster to run, with less fiddly little bits.
2) Don't tweak the formula too badly. Instead of overhauling spellcasters (or fighter-types) to bring them in line with each other, address it on the detail level. Change the effects of spells at the numbers level (reduced damage, reduced duration, etc).[...]
I feel this is pretty much what Pathfinder already did - you are describing the evolution from 3.5 to Pathfinder. It could do with another iteration, but the end result would only be a little different. Many times when people criticize Pathfinder for being too little, too late, I feel they have not really realized all the little spell changes they did from 3.5, the many spells who had reduced durations.
First suggestion-Kill feat chains. Tie them up, lock them in a safe, throw them down to the bottom of the Marianna Trench, and never speak of them again. There is no reason my grapple-based Fighter needs about 8-9 levels worth of feats to finally reach being passable at grappling something.
I support this.