You can play the Imerial Campaign, but with the unit changes of RTR. The main differences, being a removal of the Wardogs, Screaming Women, and other 'fictional' units. Also they added loads of units to the different factions, changed the general bodyguards (triarier for Romans, and heavy Hoplites for Greeks, still Noble Cav for Germans and Gauls, etcetere.). The German Spear Warbands lose their phalanx formation, but another unit is addes that is more expensive which fills the same role.

There is a new Provincial campaign which adds territory (bigger map) and a lot of new cities.

The crew at RTR are working on a version 6.0 which should be out soon, if you want to wait. Otherwise, if you really like the germans, keep vanilla total war, if you want to play more with the variety of Roman units, try RTR, also with Carthage, the Lybian Spearmen an now form Phalanx, and it makes the Carthaginians tough for once. Haven't many others, Thrace is harder, but very fun as you are always fighting skirmisher battles. Egypt gets some Hoplite and Pike mercenaries (don't know what else, those are all that i have battled againgst the Ptolomaic Empire).

To answer your question, no you will not be able to play the same game. You can install Rome Total War twice, I do this mainly to try the varying mods, some of them are very nice, and fun to play.