It's hard to say as I'm having to balance fond memories against a current gameplay experience. I have not been able to get STW working for around 8 years now. The two Shoguns are the only TW games which I have found to be atmospheric, the others always felt rather generic and gamey due to the need to cover multiple cultures.

I'm able to name many examples of what worked for me regarding STW's atmosphere, and most of those carry over to S2. In some cases it's a modernised version, like the agent movies, interface visual design and unit artwork. In other cases it's an exact copy, like the samples of STW's music on the battle loading screens. There are a few cases where each game presents an individualised piece of atmosphere, such as STW having its campaign map laid out on a table and S2 having its fog of war act like a brush painting. In those cases each presentation works well.

There's only one case where I can think of something STW did better, and that's battlefield mists. Modern fog effects don't quite have the same look to them as the effect is processed differently. There was something haunting about a foggy battlefield in STW ...