Ideally, the player characters should be able to do more than just be generals deciding tactics - they should be able to influence the outcome of the battle with their actions alone. A mid- to high-level paladin should be able to whip up on a battalion of hobgoblins single-handedly. The PCs should definitely have the chance to be the true heroes of the battle, and become the stuff of legend.
Some thoughts: 3.5 Dungeons and Dragons places an emphasis on miniature-oriented table top rules. Whatever you did would have to be born out of that orientation.
One of the things L5R allowed for (if memory serves ... I usually end up fudging in favor of dramatics) were moments like fighting your way through to the enemy leaders/heroes for a dramatic showdown, capturing the enemy’s standard (of dubious use in a non-samurai game), stopping a rout, that sort of thing.
This would be a great place to introduce some new feats and skills, and to make the charisma stat not suck.
12 levels in fighter? Charisma was your dump stat? Guess that Aristocrat/Expert with an 18 charisma and the leadership feat is going to whoop all over your sorry army!
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