It's a toss up, but I'll go with Rome. I prefer the period and diversity of Rome, but MTW2 is a very close second. I played the first Medieval religiously for two years, then switched to Rome. Medieval's map, the aforementioned re-emergence, lack of internal sea trade, and some lame AI 'tactics' just annoyed me to death. No loss for me when those were changed. It was an excellent game, though, and ushered me into the Total War series.
Edit: And the lack of Chinless Wonder REALLY bolstered Rome when I played it.
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