So if I was to remove 3.5 Fighters, Barbarians, Paladins, & Sorcerers, and used PF versions instead, they would all mix well with the rest of the core 3.5 classes?
You know what? Just use all PF classes instead. All of them were improved. For instance, I'm playing a druid. The ability to choose 1 cleric domain instead of an animal companion was very nice, and I took it. Also, Wild Shape has been substantially changed due to PF's new polymorphing rules, which should make it much simpler to use, though I'm not high enough level to use it yet.
And Clerics were improved greatly as well... now that they can Channel Energy to heal, they can use their spells for something besides Cure Wounds.
And Cleric domains, Sorcerer Bloodlines, and Wizard specialties almost all provide a basic attack mode usable 3+ main ability mod times per day that is preferable to resorting to a crossbow after you've fired your 1 or 2 spells for the day at 1st level... now you have an additional 6-7 firebolts/force missiles/etc before you have to resort to weapons.
Also, Rogues get a lot of cool choices for additional abilities at much lower level than 3.5, which can make each Rogue more unique.
The point is, every class is improved and given more options, more things they can do. I know that if I were in a game that said we'll be using these PF classes and these 3.5 classes, I'd always pick a PF class. Just do yourself a favor and use all of PF as the base, and then throw in some additional material from the Spell Compendium, Complete books, etc if you want. That's really the best way.