Here's an idea. An XCOM, or at least, XCOM-esque mod.
By that, I mean, soldiers are individually much stronger, but also, a lot LOT harder to recruit. You can't just go to any old village and get a full army.
I'm not quite sure how you would get them instead... maybe just have a lower party limit so the soldiers are more important?
Either way, the soldiers could use a levelling up system sorta like that Chinese WW2 mod, where you need stuff in your inventory to give to them. The reason is that the 'alien' or at least 'badguy' faction has vastly superior equipment to anything you can buy, so you have to kill them in order to get the good stuff.
Also maybe a Solid and Shade style system, whereby you can trade the enemy equipment for unique armor sets and such.
The idea is that, just like the XCOM series, you don't have a big army, each death is a major impact, and the enemy is vastly superior until you can take advantage of the stolen equipment.