I've said it before and I've said it again. Civ needs an extra layer between unit and map.
Cities build units. Units are not directly visible on map until combined into armies. The number of units per army (and the number of armies an empire can support) can be increased with tech/civics/governments/wonders/etc. Armies are limited to 1 per tile. A combat between two armies is resolved wholistically, that is, it behaves differently than pair of units from opposing armies fighting one at a time. This combat would be automated (no Total War style being directly involved in the tactical level). But it would probably be shown in a diagrammatic way on a popup screen (unless disabled of course). Think like what EU4 or CK2 has, except that it would take place in a single turn.
Elements that would come into this army vs army combat resolver could be: front line and support units in the same army complementing each other, relative composition of the two armies, size of the armies, terrain the battle takes place on (and possibly adjoining tiles to), tactic assigned by player to the army prior to battle (ie, charge the enemy, attempt flanking manoeuvre, etc).
The idea is that micromanagement and clutter are reduced, and the strategy and tactical layers are both explicitly present on different levels, but connected. An army with lots of cavalry might move faster and be stronger if it has lots of empty grassland tiles around where a battle happens (to represent flanking opportunity), but be weak against an army with lots of spearmen defending a hill. The player is involved in strategy by picking tech, which units to build armies out of and deciding between lots of small armies and a few big one. And is involved in tactic by positioning armies (there would be a handful per side per war) and assigning tactics to armies.
In other words, the simplicity and efficiency of multiple units per tile is kept (few stacks to move around), while the tactical elements and decision making of 1UPT is kept (but represented in a different way).