Heres a list of things I dont like about D&D 3.X
The Magic System, I hate the whole spells per day thing
A few things have happened to ease the pain but it's absolutely still in place. As mentioned above, cantrips and orisons (0th level spells) are at-will as much as you like. Additionally, most spell-casting classes have other abilities which they can use many times a day that give them at least something to do that isn't "fire a crossbow". There's no per-encounter spell mechanic like 4e though.
That would be a decent place to throw in a house-rule. All crits auto-confirm. That was easy.
Not sure what this means. I can say that in PFRPG, characters get
more hit points. You get to pick a favored class at 1st level and all levels you take in that class give you an extra hit point (or a skill point - your choice). Also, Toughness as a feat gives you what amounts to 1 hp per level (though you get your first 3 all at the start). Also, you die at negative <your Con score>, so for most it's deeper than the old -10 figure. Also, there are spells like
breath of life that allow penalty-less raising within one round. Also also also, raising the dead doesn't have the mechanical penalty it used to.
You're going to love this: there's no multiclass penalty in PFRPG. (Aside from not getting your favored class bonus hp/skill point.) You can mix & match all you like.
Skills are much like 3.5 only with some consolidation. Hide and Move Silently together are now Stealth for instance. Also, the choice mechanic is simpler but 100% compatible. You don't need to dink around with class vs non-class skills the same way, which is awesome.
The monsters have been revised, which is probably the hugest PFRPG change. Eight years of learning what was
wrong about various monsters. The bestiary is awesome.
That's a DM/plot thing, not a rules-set thing, really.