I have not played RTW that much (something like four campaigns) and it was a while ago (only played the vanilla version) but as far as I can remember the main negative points were:

a. Strategic map
- AI can fundamentally not manage it and it's difficult to make sense of some AI move;
- micro-managing assassins, diplomats, etc takes even more time than in MTW
- AI cannot cope if you send assassin on sabotage mission
- too many meaningless skirmishes against bandits and orther faction (nice wy to get new generals but tedious after a while)
- almost impossible to keep track of too many v&v
b. battle map
- AI very stupid (quite a few times it will stay idle while you are peppering its troops with javelin and arrows)
- sieges are a big joke due to AI incompetence

as far as I remember I lost one battle in four campaign and that was the first time I had to deal with the celts and their chariots (as a matter of fact they pretty dealt with me on that occasion cause that was one of my most crushing defeat ending up wondering WTF had happened long after the very short fight has ended)

Not saying there is no fun possible with RTW or that MTW is just perfect but just enjoy MTW a lot more