I really can´t say, I like both Medieval and Rome, each has its highlights. While the battlefield AI in MTW seems to be better and the battles themselves are slower, some of MTWs battles tend to get rather tedious, since only sixteen units per side can take part at any time, which means that the big battles are usually one massive attack and then an endless tickle of reinforcements. But at least the battles are decisive (i.e. if you win, you´ve got the province under your control and just have to siege out the castle). The matter of sieges is similar - in MTW, they tend to get rather dull, but what potential they had in RTW (due to the siege engines) got a bit wasted for pathfinding reasons, a poor AI that undermans its cities and the fact that it´s possible to starve out a city without a single loss.
However, I prefer the strategic aspect of the RTW battles, choosing the terrain and the possibility to make use of multiple stacks fighting in one single battle (despite the lag that causes). On the whole I do prefer the RTW strategic map, though army movement by ship is a real pain, I believe even back then it was possible to go from Londinium to Alexandria within half a year.
City building in RTW is much more streamlined than in MTW, which I believe to be good, as it gives the AI access to high-quality troops eventually and makes for better balanced AI armies. It does, however, limit the need for strategic planning from early on which is so crucial in MTW (where it is even even more focussed due to the regional valour boni).
On the other hand, while RTW has way more diplomatic potions, it´s almost impossible to utilize them properly, due to the AI faction behaviour (often I was offered an alliance only to be stabbed in the back the next turn, it seems like there´s a hardcode that demands a backstab).
Finally, the game goals, I think RTW has the better solution, and BI does improve that even more. In MTW you either have to conquer the whole map (conquest) or wait till 1453 (GA) where especially the end-game phase tends to get a bit dull - no enemy can stand against you, the few real challenges are the faction re-emergences (which are a great plus of MTW - I like them a lot), while in RTW you have at least the civil war against the other Roman factions (if you´re so lucky that you can anger the Senate to the point of outlawing you while you don´t have the fifty provinces already, something I´ve never managed ).
So, in the end, both games have an equally well-deserved place on my harddrive and I tend to play them interchangeably.