I do like the OP's idea, but as far as historicity is concerned I think it's a bit of a no-no. In sandbox it may work, but definitely not in the campaigns, which are essentially there to tell the story (in general).
A skirmish mode would be excellent, though. I, too, love the Total War series and the battles there. The idea that you can set up a game, choose a battlefield, choose armies, then actual units, and then pit them out in your own what-if scenario is just great (in fact I look around specifically for games with a skirmish mode). With Hegemony's battle system it would be pretty brilliant.
Having said that, I have had some huge battles in this game before.
Once, I was in the area around Pella with a large force (10+ units) in the field plus units in my cities when the Greeks arrived in one of their many coastal raids. Another faction turned up, too, and were fighting both me and the Greeks. I filmed it, with the intention of putting it on YouTube, and the song I chose for it was 8 minutes long. Even then, the battle had to be played at close to double speed in the video just to fit the music. Unfortunately I didn't put it on YouTube.... :(
And today, I was in sandbox as Sparta, and had been getting harassed by troops from Messene, so I mounted an assault. I sent in 6 units of hoplites, 2 units of spearmen, and one of catapults, but split them into two groups and attacked from two directions. Naturally, the soldiers inside Messene came out to attack the 3 hoplite units that had got there first, and while they were being slaughtered my main force arrived from a different direction and directly besieged Messene. All was looking well. Due to lack of space around the city, I had spare units to run around capturing the outpost and farms. Just as the city's points were getting close to zero, though, a similar sized Messenean force arrived from somewhere else and there was a second battle going on, in addition to the siege. I lost in the end, but it was a really epic battle.