- Area of Recruitment (AoR) - A means by which the assimilation of foreign peoples is simulated. Essentially if you are the Romans, you can't capture say, Carthage, and imediatly start using it's military and other facilities to pump out Roman troops. Instead you must first assimilate the conqured population via three buildings which succesively let you build native Auxilary troops and eventually troops belonging to your nation.
Elimination of ahistorical units - This is kind of subjective, since certain things which where eliminated had been actually used in war at some point or another. Mostly the fact that units such as attack dogs, screaming women, chanting druids, and flaming pigs never were never part of organized military forces led to them being removed.
Unified Rome - The Senate and Roman Houses are gone. Though I kind of miss playing politics with the Senate, the game is better for it.
Earlier starting date - Now the game starts on 280 BC. The Romans have to work to unify Italy, and they have to deal with Greek presence in southern Italy as well as Phyrrus of Epirus at the head of a large army.
Larger map, many more provinces - Not only are more provinces added to the original map, it has also been expanded to the north and east. Scotland is now whole, and you can see the full extent of the Selucid Empire.
Different factions - The Britons are gone, Thracia and Dacia have been merged, Illiria appears, Scythia is replaced by Sarmatia, and now you can play the Bactrians. All previously unplayable factions are playable (exept rebels). Also the factions themselves have changed. Carthage is now bigger and more powerfull, as opposed to the wimpy version in vanilla RTW. Egypt is now the historically acurate Ptolemaic Kingdom with apropiate units. The Selucid Empire is now gi-fucking-gantic, but a pain to keep toguether (think Holy Roman Empire back in MTW). Various other changes.
More realistic units - Self-explanatory. Examples include: no Lorica Segmentata (shiny armour made from metal bands) for Roman troops as it is inapropiate for the time period. The Parthians only have archers for foot units, any other foot soldiers they need will have to be raised from conquered populations. You can no longer use peasants with daggers and pitchforks as troops, good ol' poorly trained militas are still available. Elephants not so invinsible provided you have javelinmen handy. Etc.
Mercenaries are more plentiful, and thus play a bigger role - Need a lot of soldiers in a hurry? Have lots of cash laying around? Short on expandable cannon fodder? Hire yourself some Mercenaries! You can now also regain lost merc troops at you local barracks, take advantage of this new feature now!
Other stuff
I heartily recommend Rome Total Realism for everyone and anyone playing RTW. It truly enhances the gameplaying experience. Though by the looks of things, Europa Barborum (I suggest you look at the "Countdown to Open Beta" threads) will blast RTR out of the water and render it obsolete. However, RTR is pretty good while we wait for EB to be released.
Good news! It's over a lot sooner than expected!