Cool thing: I think that they are completely compatible with each other. These are what I would call as 'setting books', so characters made for one game can be easily reused in another. The game is fairly dynamic and as far as mechanics goes I would classify it as "if you can count to ten, you are savvy enough to play the game".
Personally, I don't like Star Wars, especially that whole 'extended universe' stuff and my default response to anything is "was it in the movies?". But I can appreciate this: even though the setting isn't my favourite in any respect that matters to me as GM, books provide enough fluff to make it lively.
3.5 with a lot of tweaks, actually addresses the imbalances between characters. While spellcasters are still above and beyond warriors in raw power you can still have fun with it. Many skills got a bit streamlined (therefore rogue's Int + 8 skill points is less of a boon) for better or worse.
Character races and classes got the serious revision. Everyone has more goodies, abilities that fit the character style and you can add archetype that modifies it. For example, you can be a Ranger, archetype big-game hunter and play as a jolly brit hunting chupacabras with your manservant :D. Book encourages making your own tweeks and offers a selection of fairly balanced choices. IMO that's soooo much better than that fucktonne of prestige classes that flooded 3.5.
I'm very biased in favour of Pathfinder, but I would hazard a guess that it's entirely dependent on you and your party. If you like 3.5 and don't mind the fact that characters start relatively stronger and more rounded, you will most likely enjoy it. It offers a lot of customisation and provides many options from the get-go, so that's always nice in the RPG.
I'm gonna need more info ;). X-Com is good and worth trying.