@Isabelxxx
Thanks. I'm not sure if I'll do it that way, but I'll think about it later - currently I'm having RL issues and haven't been able to mod at all. Currently it's just 1 XP on my working copy but I didn't test it or anything. One note, however - at this point of development I'm not concerned about savegame compatibility. There are other changes coming that break savegames, and there will be more later.
@Silver wizard
The code for creating new vassals and giving them cities is really complicated and full of hacks. In-game workarounds are fine, but I can't really make it completely "free" to manage as you want.
About subduing: this is correct and realistic. You can convince some weaker clans to join, others won't surrender and have to be destroyed.
You don't play as shogun - when you become shogun, the game ends

Masters forcing their vassals' religion is OK, but can be done through diplomacy.
Vassal uprising - it's in, actually, but only as a single historical event. It's rare - for this to happen AI Oda Nobunaga must successfully capture central Japan and die (Historical setting helps obviously). Depending on the situation several new clans may be created: Toyotomi, Akechi, Maeda, Shibata. Making it a generic event would be extremely difficult and crippling for the AI, so I'll probably leave it that way.
Japanese calendar is already in-game but turned off (You can see it when your leader dies though, in the popup text). There are two problems with it:
1. it's unfamiliar to pretty much everyone and non-linear, so it's difficult to track game progress
2. Japanese calendar uses important historical events (like change of emperor or big wars) for eras and year numbering, therefore the actual calendar is simply wrong because it doesn't match in-game events; it could be made to match these events, but then it would be a made-up calendar...