Shogun 2: Total War - Fall of the Samurai Cheats
The best TW game in terms of modability is Medieval 2 (With Rome coming in as a very close second).
The best TW game in terms of scale and empire building is, without question, Empire.
The best TW game in terms of quality, fluid, satisfying combat and multiplayer is, without question, Shogun 2.
Personally, I prefer S2 to all the previous TW's. Steam's telling me I've spent 362 hours in Empire, and 372 in S2, and considering how I've had Empire far longer, that says it all.
The Fall of the Samurai expansion is magnificent. They're now making Rome 2 (Which I'm looking forward to in a huge way), but if they made an Empire 2 but with the quality and mechanics of S2:FotS, I'd be set for a long time.