Maybe make the penalty for overcrowding more severe for mountains?
Separate discussion, please see the thread on overcrowding, but yes!
Or allow only a certain number of men enter a battle happening in a mountain region?
Nah, let them attack with as many men as they want. They won't be able to hurt you with them,and then you can pull a 300 style victory and laugh in their faces while the rest of your forces hit them somewhere else.