Rather than add complexity to the invasions, I'd focus on the soldier job. I like the army-limit-by-species-pop mechanic but it doesn't go far enough.
I've had a lot of false-starts thinking about this but I think armies ought to use the same "naval" capacity produced by soldier jobs. Conquering a lategame stronghold planet should cost more than the couple dozen energy upkeep on a massed army (and the one-time investment of a few thousand minerals). It should be a trade off of army investment vs orbital devastation- most of which is already implemented, if poorly balanced!
As a sidenote, I never build barracks/strongholds. I get all my naval capacity from anchorages. I think the existence of anchorages should be entirely scrapped. I'm not saying they're overpowered, mostly that I don't understand the fluff of a civilization with NO soldier class but a galaxy-dominating navy, oh and also as much ground army as I care to make.
Going too far: I'd like a "mobilization" policy which sets the number of soldier jobs per barracks. These soldier pops would be specialists, partially because I think it's accurate... but also so that demobilization leaves a bunch of specialists ready for tech jobs *or unemployment/relocation*. There are multiple mechanics for handling such pops, I think that's an interesting and fluffy thing to deal with post-war. If you even demobilize - militarist empires should get unity from them regardless.
I also think it'd be cool if having excess naval capacity/soldiers could aid in boarding enemy ships to neutralize/capture, potentially as a counter to artillery battleship spam, but I haven't nailed that down and I guess the devs are already rebalancing that with the new ship categories.