Well I've always been a supporter of reverting Sci abilities to Exotic damage but if that wont happen I've been thinking about something else.
It seems in a lot of cases no one cares about Sci ships, I've seen over and over about giving Cruisers a new type of weapon or giving them more of a advantage with the ones they have. Now Cruisers can do some nice damage if built and flown right but most Sci ships suffer except maybe the Vesta line. (And that has a lot more going for it than any other Sci ship in the game.)
A lot of the various energy weapons are called *particle* weapons. Phasers, Polaron, Tetyron, and Antiproton weapons were all particle based weapons.
Basically what I'm getting to is maybe Sci ships can get a new little innate buff that allows energy weapons to gain some damage from particle generators.
Doesn't have to be a huge buff but something would be nice!