isometric vs top down; crap menus, crap graphics (yes you read that, imo civ wins in style).
I really think the first one is better, a lot better. Its like AoE 2 vs AoE 3, imo they broke the third, whilst the second remained better and still does to this day
In so far that I can play and love the first (even still, really, i had to dig it out and release it last year), but do not play anything beyond it. 2 was a disaster (a real mess), 3 i hated, 4 is slightly better but a pale shadow of the first. Shame really. My little brother likes the fourth though, but its a bit like Pirates! remake, pirates! is better than the remake imo once again. Maybe its a Sid thing?
I believe they are making a DS version, maybe i'll get into that more. I'd be happy if they just ported the first though.
On to total war:
Medieval 2 is an improved graphics engine, and AI bugfix plus a few new character types over Rome. It wasn't a 'revolution' like Rome: Total War was that overhauled and vastly improved pretty much everything, in so far that its really, really different to the earlier once and got a shit load of critical praise because of it. I play these games a lot because of how great they are as sandbox games. I do get numb to them, and give them a break but i can always get back in.
Unlike civ though, they are really a solid refinement so even though looking back i'd choose Rome as the best, the improvements and refinement in gameplay means i won't play it anymore because Medieval 2 has more fixes. It was criticised for not being as big an improvement though, and you can argue that historically you don't consider the time as interesting, both happen, but its pretty much a very solid refinement.
Rome is a vastly, vastly superior version to shogun though. Medieval 1 was more like shogun, but Rome was a complete overhaul. You should really look at it, it doesn't really play like shogun. In fact I never liked shogun total war and think its probably the worst in the franchise.
In related news, Empire: Total War just got announced:
They finally fixed the sea battle issue so they'll be in real time too. I want a multiplayer campaign though, sure the campaign map is turn based but civ did it for pete's sake.