I don't want to have a million troops crammed into a single square mile. On the other hand, i always felt that having a cap of like 9 units or whatever was kinda silly. If you want to really heap your troops up, you should be able to. The logical counter is the nuke or magical equivalent, as KillzEmAllGod said. Stacks will then have a natural organic cap rather than a hard cap, which is much better to my mind.
Want to put all your units in one spot? you can do that, just expect the other guy to use all his nukes in that one spot and blast them all to bits.
Make the game landscape force large empires to snake through undevelopable land features so that empires have multiple borders. Make armies slower and slower the larger they become. This forces large empires to split up their super stacks to protect other strategic interests, rather than because there is an artificial unit cap.
Not really. As long as they leave just enough basic recruit troops to hold their cities, they can afford to stack everything else into one spot, and even if they only move at 1 tile per turn, that dosen't mean they can't totally crush another player. Even if they move incredibly slowly, a stack like that will not be stopped by throwing barbarians or small stacks at it. And when it reaches the other players cities, his only option is to make his own super stack to fight it off.
Super stacks are so common because the only real counters to one are high powered overland damage spells or another super stack. Think glaciers. Ya, they are slow, but they really mess up the area as they move through. Valleys dug, mountains gone, or created. Slow but strong works just fine.
Even if having a super stack crippled your economy or defenses, as long as it can attack before your empire falls apart, the only way for another player to counter it is to make their own crippling super stack.
Although forcing armies to travel through rough terrain in between empires sounds great. Would be fun to set up ambushes or traps in those areas. Although it wouldn't really deter a super stack.