I went in with four XECs (2 4xLascannon, 1 shield, 1 rocket) and two hovertanks (Lascannon), one Termicator, and the rest filled with Annihilator (15, I think). Everybody equipped with Battle Lasers and Riot Shields.
The surface was surprisingly easy-- sent out a hovertank to get eyes on the enemy, then a Paladin to soak up damage (and jiggle back and forth to absorb reaction fire), then Termicator to take advantage of better vision, then the heavies to clear the landing area. Then it was a pretty vanilla hop from bunker to bunker, with the XECs going out in groups of two, leapfrogging each other to give their shields a break. HTs were used as spotters.
Base assault was normal-- easier than a Mercenary Base since you can bring vehicles in... though they also get to take their heavies (Sectopods). I switched from my own Battle Lasers to looted Plasma Rifles (70las vs 80plas) since there was plenty of ammo, and it was marginally stronger. Never used my Imperator missiles...
Across both phases, I only took two damaging hits-- one was during turn 2 of the surface (Mercenaries managed to destroy 800 points of
blue shields in two turns!?), and once in the base when I made a bad call about if an area was mostly safe... and overreached a foot soldier straight into a Sectopod. Sent a hovertank rushing across the map to cover her, which lost all its shields and half its life, but not a big deal since I took out the Solar Governor the next turn.
Final score:
Yeah... about that one lost hand... I wasn't paying attention and sent a CLAW against a Marsec Gunboat. Then accidentally quicksaved instead of quickloading, with my last save being about three hours back. Oops.
If I paid more attention to the tech tree, and my RNG wasn't godawful suck, I probably could've shaved upwards of two years off. More, if I didn't invest a bunch of resources into things I didn't do-- I basically skipped all of advanced VooDoo (never even got my Codex's specialty armor or weapons) and did only half the Witch's Coven.
Once you start getting access to tanks (and better), the ships to carry multiples into battle, and you don't care about prisoners... difficulty level drops
way off to the point it's not really interesting anymore; it turns most battles into a one-sided slaughter, and the ones that aren't, tend to mean that you're getting shredded by enemies that outclass you-- Marsec is
nasty... At near-endgame, it took around 8 gals using their entire turns to kill a single soldier. So I just grabbed his stuff and ran, like I'd do way back at the start.
Ninjas were mostly just
annoying than problematic-- new ship alert spam, having to route around them, a bunch of extra missions that weren't particularly rewarding but took forever, etc. I'd be happier without it, or maybe adding an ending to their storyline as a lesser victory. I do like how, even incomplete, it's obvious that there're intended to be multiple endings, and that Cydonia is probably the 'normal' one.