I never played the original shogun, but I did play RTW and M2TW, and I think the thing I would like to see most is better battle and campaign AI. In the campaign AI it would be really cool if the AI had the ability to think in the long term and set long term goals as well as think in the short term.

I would also like to see an improved, more in depth and more realistic diplomacy system. In RTW and M2 the diplomacy consisted of sending a diplomat over to a faction, clicking a choice and seeing if the AI accepts. In S2 I would really like it if the diplomacy consisted of actual negotiation, the ability to coordinate attacks with your allies, conduct trade, etc. If done right diplomacy could become a very important and fun part of the game.

Family politics should also play a big role in the game, because AFAIK they played a huge role in Japanese politics. It would be cool if all FM's would marry FM's from other clans in the game, and the player could attempt to set up these marriages. Of course this could become tedious so I think that marriages should also be able to happen on their own without player direction. However, if a feature like this were to be implemented I think it should not use agents like in M2TW.