No stacks of doom. If a unit in a stack is destroyed, then all the units in the same stack are destroyed as well. This forces you to spread out your units instead of clumping them all together.
And since SMAC is the best Civ game out there it also comes with the system: when a unit in a stack is destroyed it explodes and deals collateral damage to others in the same stack. This way you don't lose your whole army in one shot. It will take several successful attacks to kill the whole army.
You can also give Call to Power 2 a go. It's a bit rough around the edges but it also solves the stack problem elegantly: each stack only has a maximum of 12 units. Not only that but you need to combine different types of units (melee, ranged and artillery) in order to make it a viable combat unit. Look up a gameplay video to get the idea.
Honestly Civ 4 is the worst game when it comes to combat thanks to the ugly stacks of doom (TM), whose problem is exacerbated due to the lack of control zones. Personally I find it unplayable without mods.