Well, for large battles, Rosebud is the battle of choice over Little Big Horn for me. It lasted longer for the main battle (the Reno Hill portion of LBH of course went much longer) and included two different cavalry regiments and two different infantry regiments mule mounted and included Crow and Shoshone allies for the army. LBH may have lasted in minutes rather than hours for Reno's action down below his namesake Hill and Custer's annihilation (some accounts give it maybe 15 minutes to wipe out Custer's force). And virtually the same Lakota/Cheyenne as at the LBH eight days later.
And it is my contention that Rosebud and the ammunition expended by the natives saved the 7th from being annihilated completely, not just Custer's battalion. Some say the natives replenished the ammo on raids and from dead but there just weren't enough dead troopers or time for enough raids to do that in those intervening seven days before the other battle on the eighth day, some replenishment, yes, but not enough - and Custer's men no doubt expended most of their ammo in a desperate if futile bid to survive.
As to smaller actions and skirmishes, there were many - later I'll find my book that lists lots (most?) of the actions and post the title (wife sleeping in area where shelved). However, recommend you look at the Nez Perce war - it has a number of battles. Also the Modoc war - with a very different modeling environment for a table top. You can also do tribe versus tribe skirmishes. The one to avoid is the circling the wagon trains - more of a Hollywood thing. One I know less about but the Seminole war is another different environment for modeling.
And, of course, there is the delightful Battle of Whiskey Hills as portrayed in the movie Hallelujah Trail! No, not historical but where else can you order your troops to "Protect both rears simultaneously" while pointing in two directions at the same time?
And well to remember that Indians did not fight to the last man, they fought either for raids, for honor, or to protect their families. And minimal casualties was always of critical importance to them. The closest I've ever heard of them doing anything 'military' was the way the Shoshone 'marched' into Crooks' camp ahead of Rosebud. But they didn't fight that way.