Yeah, as good as Shogun 2 reviewed it was surprising that Rome 2 was so terrible. No hope for Medieval 3, huh?
Shogun 2 largely worked because they went back to basics. The topography of Japan meant they didn't have to stretch their campaign AI, unit rosters were virtually identical and outside of some limited RPG mechanics there wasn't a vast amount that was really new there compared to previous games... and even then there were issues on launch. Rome 2 was a massive revolution and much like the last time they tried that (Empire) it all fell apart rather quickly.
I could spend hours picking apart the flaws in that game but one is fairly fundamental; the engine. The TW Engine they used for Rome and Med2 was designed for armies primarily engaging in hand-to-hand combat while holding formation and ranks. The Warscape engine was designed for the combat in Empire; units firing muskets at each other while canons fired overhead and hand-to-hand combat was more between individuals then it was between units. That didn't work particularly well in Empire or even Napoleon, it just about held up in Shogun and it completely disintegrated in Rome 2. Combat was reduced to big blobs of soldiers wildly slashing at each other while you did the most basic tactics possible and spammed the MMO style rechargeable abilities. Unless they've worked out how to get the Warscape engine to accurately deal with formation close combat then it's always going to be a struggle to cover that in a game.
I'm not entirely pessimistic about a possible Med3. We'll learn a lot from Atilla. In the same way that Napoleon was the game that Empire should have been but on a much smaller scale I hope that Atilla is the game Rome should have been but on a smaller scale, fixing most of the issues. If they do make Med3 and they do basically what they did with Med2 from Rome (keep the basics the same with a few new features) by building on what will hopefully be a successful Atilla then it should be fine... I'll still wait a while after release until the early bugs have been sorted and the first few mods have come out but I won't be too unhappy. If they try to revolutionize the series again then I'll probably wait at least a year before buying.
(On a side note I'd add that Rome 2 reviewed extremely well... at least to begin with before the backlash began... which says a lot more about how games are currently reviewed then it does the game itself)