ship Base abilities:
hacker: Hacks enemy base, unleash computer virus lowering def by 10%.
Biologist: unleash engineered virus, disables shield charge and base loses 4 ability points.
Spy: sends out a spy drone to gain Intel, attack and def lower by 10%
fixer: boost allied ships hulls
governor: adaption, boost allied def and attack by 10%
raider: adds 10% to allied ship when raiding the base
saboteur: disables one weapon, or defense, or shield mode
still thinking of ones for: builder, merchant, miner, excavator, physicist

New base abilities:
Deploy's ship fleet: spawns a 10 man boss npc with unique drops
Concentrate all fire power:base loses 20% of defense but gain 20% in attack
Don't let anything through: base loses all attack but gains 10% defense
well, this my general idea obviously it needs alot of work and the numbers and percentages to be adjusted.

also, while i'm posting suggestions, here is my thoughts on how to improve the game:
large increase of new npc, this is what i enjoy the most and right now there is no reason for me to farm nps. Perhaps adding mythical npc with uber rare drops, as well as new npc that unlock missions.
PVP please can i get some ranked payers, i have increased my scan to the max and still only get guys 100-300 ranks lower then me not fun!
Ship designs: I feel like there should be more work involved in creating a new ship other then earning one VIA achievements. Also, its completely irrelevant to me unless they add some kind of boost to a ship stat. I have no desire to aquire them unless they do so.
The galaxy legion market could use some changes as well, such as 48 hours sales on limited edition items, should boost your sales as well as get the game more interesting and fresh.

oh ship abilities would have a 8 hour cool down and sabs would have a cap on how many structures they could disabled. so if your legion had 8 sabs, they all couldn't sab; the cap would be at four or something.

some of these are pretty good. i like the idea of being able to hack a base. a +1 for that.

the bit in green i agree which would be awesome, but the stuff in the red color u would need to elaborate a bit more or i don't think they would do good in this game

What's highlighted in red is WAY too powerful. Instead, it should decrease shield recharge rate by 10%. And what's highlighted in green is good, but would need some limits to make them reasonable. The hacker ability should last for half an hour or so, the player has a two hour timer on it, and it cannot be stacked (i.e. a base debuffed by a hack cannot be hacked again until the debuff wears off). Similarly, the spy drone would last 30 minutes, have a cooldown of 2 hours, and cannot be stacked.

The fixer ability might increase the legion's hull bonus by 10% for 15 minutes with a 2 hour cooldown, cannot be stacked, and cannot be removed by a c missile. The adaptation would last for 15 minutes with a 2 hour cooldown, cannot be stacked, and would be immune to removal by c missiles. The raider ability would last for 15 minutes and have a one hour cooldown.

Merchant: Steal 5% of that days base output during raid