As I see it:

STW Pros (vs MTW):

-Atmosphere

-Ambience

-Better definition of the spears/swords/cav system

-More difficult campaigns

-Better balanced battles

Cons:

-No V&Vs for generals

-No statistics apart from command for generals

-Hojo Horde effect (one faction dominates central and/or eastern Japan, leaving you, if you're playing as one of the western factions, facing a huge opponent, or lots of rebels.)

-Geishas

-Suicide Daimyos(sp?)

-Small unit roster


Personally none of the cons for STW really bother me. For me it was and still is the original and best Total War game, that has yet to be entirely surpassed. Sometimes a huge range of hundreds of different units is not needed, and detracts from the gameplay. STW was all about strategy, with the underlying Sun Tzu thing. With MTW there are units that upset the balance. There is also this culture of building up a certain 'uber unit' and just fielding it exclusively using bumrush tactics. STW didn't really allow for this style of play. I've often read threads about MTW MP and seen remarks about not using any spear type troops at all. This indicates a serious inbalance and shouldn't be happening.

I also feel that STW was better before MI. The Kensai and Battlefiled Ninja (complete with cloaking devices, since ressurected as 'hashishin' in MTW {And guess what? it looks likely that something similar may emerge in M2TW in the form of "Battlefield Assassins".}) feel a bit 'kiddy'. The mongol campaign was also lacking. A pity the developers didn't allow the mongols to construct buildings this would have made the campaign at least half worthwhile playing.