Now, I'm no modder. I'm useless with anything fancy with computers. So I don't know how viable this will be, if at all.
But I think it'd be totally awesome for there to be a Korea invasion mod. Historically, Japan tried to invade Korea in 1592, so it wouldn't be out of the period range (no drastic unit mods etc) and most of the clans could be kept. It would just involve turning the Korea bit of the map into a living, breathing land with settlments etc.
You could play as a Japanese clan or the Shogunate, unite the clans armies and launch the invasion, or play as Korea and attack Japan first.
Might be difficult to pull off - I don't know how Shogun 2 responds to map modification like Medieval 2 could, but it seems like a pretty good premise to me.