I'm not really sure if this is a good idea given AI war's focus on macro over micro. Also, you tend to spit out a *Lot* of capital ships later on, keeping track of those actives would be quite hard and antithetical to the game's core design principles. Even on golems I think its better to simply build those abilities into its stats, or have them as passive aura's that are always active. There aren't many abilities i can think of that would be better off activated rather than being automatic or passively on all the time. I wouldn't want to feel obligated to go and baby sit my golem beyond giving it its marching orders, it would annoy me if I had to tab over and activate its abilities manually or it would perform sub-optimally.
That said, I'd love if the Champion Ships (assuming they even get added in 2) had many active abilities to use, unlike the AI war 1 varients which were quite boring. When controlling a single ship, is a great time to give the player many powrful abilities with long cooldown costs and slow mana regeneration. If you have played warcraft 3, you know that this basically makes every spell count and someitmes you want to not cast to conserve the energy for later.
My ideal Champion type gameplay would resemble something like a battlefleet gothic Armada ship's gameplay with some modifications, and more abilties since theres only one ship. Seomthign liek this:
https://youtu.be/lGARShXaLSM?t=472. Cool, impactful, hard to aim or situational ablilities, with long 60 second cooldowns and a longer term mana bar to make ability conservation an actual thing. instead of always spamming the moment things go off cooldown. In addition, some solid, but not quite significant turrets to mop up stragglers in a system. Oh and also make an XP and equipment score that encourages teamwork, get rid of the shadow realm, to discourage players either warping off to play their own minigame or from running in after a planet has been effectively taken just to snipe that sweet 'liberation' XP. Basically the XP has to be based on some kind of team merit that interacts with the main campaign layer, not the somewhat disconnected shadow layer, such as each planet liberated by the human team gives a level up, or perhaps even better the Champion player gets metal and research from everyone else on their team's mining (as in a free 'bonus' and not siphoned from the other player) with which to buy more equipment and abilities and Champion Techs, as well as repair or respawn the Champion ship.