I disagree, 1UPT is the best feature of CIV 5. The fact that it favors the use of small number of stong forces over a mass of weaker forces is a bonus.
The only way to have a better army before was to have more units in your stack. Spam more units than the other guys and you will get a larger stack and larger stacks win.
Now a small but effective force using terrain and tactics can deal with a larger forces that is either weaker or using poor tactics. I love the new mechanic and I'm having a LOT of fun with it.
---
That said, if you want to have unlimited stacking, but also make it so that its bad to put all your units in one stack, you would make it so that EVERY unit does collateral damage to a stack. For example, if your stack gets attacked, all units in that stack take damage. This would be best for range attackers, especially seige units, that would effectively get to do "free" damage to all units in the stack.
Secondly, you could implement an "overcrowding penallty". The simple way is a flat -15% to all units in the stack (and no flanking bonus). Better may be -10% for each unit in a stack, which mean could put 10 units in a stack, but would be at -100%.