Hey...Correct me if I'm wrong, but wouldn't doing something very simple solve the problem TheStealth brought up? Have semi low morale, but, very easy to turn on and slightly more difficult to turn on 'fight to the death'. Think realistically. If you're in the middle of the enemy, with them all around(and I don't think there was such a thing as war prisoners in Japan then...), you're not going to try and run through them and get slaughtered, you're going to fight as best you can. Also, fight to the death should infer some melee attack bonuses, as desperate men fight harder. That way, attacking routing foes would be a risk that may not be worth it...
EDIT: Also, an idea, that would truly make the mod unique(At least I don't think it's been done before...) is a way to make it so only some of the 'kills' in battle were actual kills, others were injuries that would take a few months to heal, (one turn), and others were just knockouts or wounds that would take a few days or a week to heal(ready in time for next battle.) Of course, any wounded left on the field by the loser would die, but I don't know whether the knockouts would be strong enough to fight off the enemy or escape, or if the winners would let them go, or kill them...Maybe a choice like in the other total war games, except no ransom or prisoners, but releasing them adds a trait, and the more times you do it, it can get your honor up? And maybe down eventually(if you're 'squeamish'). As well, any wounded in winter don't survive the season...so waging war in winter adds an extra level of danger. AND ANOTHER IDEA: Maybe, when you're in your own provinces, during the fall, ashigaru would suffer severe 'attrition', from the ashigaru deserting to go back to their farms? If you're in an enemy province it's not as big a deal, since they wouldn't exactly be able to make it back in time... I just think this might add some more realism. Might be hard to do though.
First paragraph, the stealth thing is beyond modding abilities, afaik. I didn't ever see a coding line that adressed it. So it would be CA's task to make something here.
Second paragraph, the injuries and wounded item is reflected with the replenishment of men. More detailled modding is in this regard, iirc., not possible. However, i'll try to look at it, if i go back to the files for a next update, perhaps there is something, i believe there was something for AI battle calculation, i mean to remember i applied such codes as well for the autocalcs, but well, they do not count for real played out battles by human and AI.
Modding is limited to just what open files offer.
Info update 24.03.2012: S2R+ does not work with the latest CA patches (15, 16) of end March 2012, means the FotS patches are incompatible with mods created prior to these CA patches. See also this post of mine.