Civ IV was pretty good with languages, but I've heard the Egyptian leader in Civ V apparently speaks modern Arabic. I haven't actually tried it yet myself, so I definitely could be wrong there. I wouldn't be surprised if Boudicca is just speaking modern Gaelic or Welsh and if Attila is speaking Mongolian. Really the thing about Civ is that its so long-reaching as far as time goes that it really does make sense to have people like the Celts speaking Celtic languages in their modern forms. This isn't the case for Rome.
Wait, that was fake? I knew the Atlantean language had to be made up, but now I'm really disappointed.

Oh well, the Egyptians in RTW times would probably be speaking Greek anyway. All the ones that matter to the game, that is.
All told, I think this wouldn't be quite as impossible as people are making it out to be. Ancient Greek is, afaik, still pretty well-documented. Latin would be pretty easy, as would Persian and Sanskrit if the map really goes as far as India. I think the only things you'd have some real trouble with would be Scythian, Gallic, Iberian, Old Germanic, all the other "barbarian" languages that weren't written down in contemporary times. Then again, didn't RS2 have settlement names written in Old Germanic? Even if not, I'm sure substitutions would be acceptable. Old Norse for Old Germanic (if they can do it for Age of Empires and Age of Mythology they can surely do it for Rome II), Gaelic/Welsh for Gallic, etc. The only idea here that I don't like is having advisers speak in native languages. Somebody who isn't a true history fan is going to get confused, absolutely hate it, then rave about it on some review site. CA is still a business and still has to pander to the lowest common denominator to stay afloat.