Are you looking for a realistic representation of medieval Japanese skirmishes, or are you open for a more fantasy style approach?
If the latter, there is simply no better system than Bushido by GCT Studios.
It's a skirmish game with between 5 and 10 miniatures a side, with some very intriguing rules, that are simply put
great. In fact so great, that my regular opponent and I are unable to stop comparing other systems with Bushido. and the comparisson has never been favorable to the other systems...
When I said fantasy approach earlier though, I should also have mentioned that there are several factions in the game (and there are many), that play without any magical trickery or other shenanigans (so perfectly suitable for representing realistic forces), but be warned; you'll be missing out on a lot of fun that way

One thing with Bushido is that it uses named characters for a lot of the miniatures, and all miniatures have character cards which are essential for playing the game.
But that's not too much of an issue, considering that the miniatures are all just gorgeous, and you don't need many for a playable faction. they are slighter and taller than most well known lines though; think Oriental Fantasy version of Infinity and you're not far off (so realistically proportioned 30mm)
Seriously; give it a whirl; the rules are available for free on their website, just like the required cards, so you can proxy when you try it. You won't be disappointed!
