well yes and no to this post. i am heavy into abilities myself. you have to get creative with it though otherwise you wont be able to.
so far off the top of my head heres a list of things an ability can do:
increase ship spead, hull points, turn spead, chance to hit, weapon fire rates, damage, phase spead, phase chargeup, and weapon range. the problem arises is how to implement it so that it works as desired, and then, getting the AI to use it as desired. (keep in mind, some abilities can break the AI if you get too complex).
You can also use entity bool modifiers to do other things such as give the ship a perminant shield mesh thats always on, make it invunerable, make the ship capturable (if you want an example of this, looks at Uzii's old planet mod, it had capturable ships). these are a few examples. now for the "what you can not do". you can NOT change a weapons animation with an ability (altho an ability can have its own animation for weapon firing, just has to be an active ability) you can not change things like shield mesh and engien effects, etc (it least not in vanilla sins, not sure what you can do in entrenchment)