From what I heard, RTR messes up a lot of the great stuff in the game, including cavalry charges. It stops cavalry from jumping over the first line in a unit. It also makes them obsolete by giving most (if not ALL) units more than one hitpoint.
I haven't actually played it, I decided to wait until EB comes out. And actually, EB might balance a lot of things out for some of the factions. The Seleucids will probably be able to stave off total annihilation, Carthage will be able to hold off, at least for a while. Germania and Britannia will be isolated in the early game, as they should be.
Some of the factions, though, such as Parthia and Dacia, do indeed get weaker. However, these factions were always wiped out in the original game, anyway.
My suggestion would be to use Mundus Magnus for the time being, mod your own game to keep it interesting, and wait for Europa Barbarorum.
We are all in the gutter, but some of us are looking at the stars.