You do work for factions, you gain standing. More standing gets you ability points.
You never use the points because you don't like the abilities that the faction has. You leave that faction for another one. Your standing with your previous faction is reduced to 0. But you still keep the ability points.
Now, from the game lore, im assuming that the corperations dislike each other. So, why would they allow you to use ability points that you gained while working with a enemy faction?
My suguestion is simple. Divide faction points into 5 groups. One group for each faction, and a group that can be used for any faction. You leave a faction, lose all standing, and access to whatever points you gained in that faction that you never used. You rejoin them later, you get access to the points you didn't use earlier.
The 5th group would be were the ability points you get for donating, or as a reward for voting, would go. If you don't intend on rejoining a faction, you could also convert your faction points into general points that can be used for whatever faction you wish. (Im unsure how they would convert though. I guess 2/1 ratio though)
Terrible idea. I have over -900,000 negative standing in one faction right now. It would take days just before I'd be able to get ability points again, and I'd essentially never leave my faction.
From someone that runs hundreds of missions per day, I'll have you know it's hard enough just to get abilities up with things how they are. Ability points should just remain ability points.