I think I would have it more like Dawn of War II and Company of Heroes, squad control but not as huge as in Total War. I could never picture wars in Fallout the size of those in Total War, but I could the size of them in Dawn of War II and Company of Heroes, and since they mostly use ranged weapons in Fallout, and you manage small squads of 5-20 instead of a group of 70+ soldiers, and since they use tactics like taking cover behind [censored], imo it would be much better. I mean, if you play with a BoS faction, you won't have that many power armor clad soldiers in the field, and then you go exterminate raider camps at night with maybe 80 people in them, and that's what just one of twenty possible squads in Total War would be. Total War are great games, and huge battles are awesome, but you don't really care about losing men until you lose too many men
In Company of Heroes (or moreso in Dawn of War II) a squad is wiped out and you get a little sad inside.
I could see Caesar's Legion with a huge army in Total War though, and maybe NCR too, using WW1 tactics. Hehe. Slaughter ensured. But yeah, I'd prefer system similar to Company of Heroes than Age of Empires or Total War. Maybe a mix of them all, though. Shouldn't be a rip-off or "Total War/Age of Empires/Company of Heroes with laser weapons and power armor"