If you've ever played Fallen Enchantress, it has a combat system pretty close to what I've thought would work for Civ. You move your units around in stacks on the strategic map. When combat is joined between two stacks, you're given the option of doing a quick auto-resolve, or fighting it out on a separate tactical map. If you chose the latter, the game selects a battlefield from among several canned alternatives based on the local terrain. The game deploys each side's units to one side of the map. The battles are turn-based (at a finer time scale), but it's more like each unit gets a turn. The turns aren't in strict rotation but governed by an "initiative" attribute. So a unit with high initiative will be able to move/attack more often than one with lower. It's not a perfect system, but it works pretty well.
In a game like Civ5/BE, this would make moving masses of units around the strategic map much easier. And it would get rid of such goofiness as archers firing over transcontinental distances at musketmen who can't fire back.