Empire is my favorite one and I'm sticking to it (probably because of the naval combat), despite how much I loved Rome. Medieval was basically "Rome 2 with slight upgrades, thus, making it really dissapointing and just as buggy and incredibly broken".
Empire has finally added some much needed changes, and since the game is still extremely moddable, we can still get our swords and shields if we want

- I know I look forward to that. Also, Maratha has elephants, so it's still a total war game - har har. CA is cracking down on the patches too and these "much needed huge patches" are coming out sooner, and quicker.
Though the reason I hold Rome equally high, is because it's stood through the test of time, and now has all these amazing mods for it that can make it even better than Empire. Look at the "Napoleanic total war" mod for example. It pretty much doesn't "age" now.
Also, try Darthmod for Empire total war, it gets rid of the whole "units standing still looking at each other, awkward moment before the bayonet stab" thing, increases unit sizes (but not to the point of unbearable for your system), gives much needed changes to naval combat, and improves all the AI.