From patch notes: Improved Ground Battle: there is now a maximum manpower that can be  deployed per turn. The limit can be increased with technologies and  temporary modified by ground battle tactics.

I spent my time last night exploring the Unfallen so unfortunately don't know what/where you need to go to increase the number. But I would guess somewhere in the military tree, as I was looking through the other three a lot last night and don't recall seeing anything in regards to this.

There are some techs that say 'increased manpower deployment' - I bet they relate to this.

Also, use siege modules. I forget the name, A2S Something something (Air 2 surface). It damages the enemy passively while you are in orbit sieging 

You still can deploy 3k of troops, but they cant fight all at the same time. 

If you deploy 3k and start a fight and loose all of the 700 troops you still can go on fighting with another 700 troops next turn. 

YOu can do this untill all your 3k troops are used up or until you win. 

And you dont even have to stay in this system with your ships. While your troops are fighting you can fly back home and get mire troops. 

I Think iths a realy importent change because the because there is a limit on system troops but not for troops on ships.