The real answer to "What's Different?" is: Just about everything.
The only thing they really have in common are the very basic mechanics: Roll a D20, add attack, compare to defence. Fort, Reflex and Will Saves. Classes have levels. Roll Initiative to see what order you go.
Thing is, even those 4 super basic commonalities have differences: Defence and Initiative are calculated differently (class based bonuses for both, armour isn't a defence bonus). No class has dead levels (look at Soldier vs Fighter for example). Reflex Save can be used to parry attacks (as can Fort for Shield Block). This trend continues throughout the system, too - things that are "common" aren't really.
So yeah, just about everything is different - the only thing they truly have in common is that they will use your D20 (as well as D12, D10, D8, D6, and D4). Which makes such a list somewhat impossible - it would be thousands of points long and end up being far easier to just read the book (forgetting 3.X, and not bringing any baggage or assumptions from it with you).