Abilities sound kinda neat, but from what I've seen I think that the core of the combat is positioning & order of deployment. Adding a third layer of ability activation might be neat, but it could muddle things down if there are more than a very small number of abilities. Maybe abilities should only be on the flagship, and only 1 at a time? I don't know if there is any sort of equipment or loadout thing going on, so I'm not sure how this would best work.
Another idea is to do "specials" rather than abilities. Automatically activated when applicable, they could be influenced by the ship class, the flagship, the sector you are in, or maybe even the specific pilot you have. So maybe a lancer class ship will get a short speed boost when told to attack an enemy who is over a certain distance away. It's not an activated ability per se, as it activates on it's own, but it isn't necessarily random chance either. So this is sort of like having "auto-cast" abilities, but still giving some more unique flavor to individual ships or designs.
Some other examples:
-When only 1 interceptor from a squad remains, he goes berserk and attempts to ram the nearest enemy ship.
-A certain type of pilot causes his ship to become temporarily invulnerable for 2 seconds when it drops below 20% health.
-If more than X boarding pods are incoming to your flagship, it gains 250% turning speed and 50% acceleration for 10 seconds.
Or whatever. Having abilities you can activate manually isn't bad in my opinion, but it certainly might make me feel like I have to play at a slower speed in order to get the timing right.