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I used assault shuttles to board and capture a vessel with a leader on it. When i tried to scrap it, the game warned me it would re-assign the leader to the pool..but nothing happened. What happened to the leader?
I think i know why the AI dont have enough ships to fight.

They spend a lot of their command points on there any way to stop them from doing this? Its pretty crippling for single player.
As for the spying. I do spying a lot. It's saving me because AI is getting ahead in science most of the time. I go for productivity tech, and then science and spying. I select the spying techs almost always. I select a spy bonus when creating the custom race. This is in Moo2.
In Moo1 I think the Darlok is the best race when playing on impossible.
Yeah there really isn't much point to ground armor forces. If you could use them to board ships, maybe.

To me ground combat is always about boarding ships. Unlike MOO1 it is extremely weak in MOO2. If you're ever in the position to be invaded then you've already lost. You can also just be bombed to death or blockaded.

Unless it's a feudal or dictatorship government I don't even bother with a marine barracks. It's just wasted maintenance.
The only use I've ever found for the Armor Barracks is to build them on Sakkra worlds I've invaded. Even with the Alien Control Center it can take a long time to assimilate a large population (doubly so playing Unification when you forgot to research the ACC ....), so the tanks/Battleoids can be useful to hold the planet.

Rebels: "Down with the Empire!"

Mech: *squish*