At first I thought, well, Science and Banter and Intrigue don't sound like things Star Control characters would use a lot.\
Then I realized, the only skills used in SC2 are Turn Left, Turn Right, Primary and Secondary
So, yeah, the focus will have to change a lot for proper roleplaying, doesn't seem that weird to focus on less shooty stuff.
Also, more off-ship stuff will definitely be needed.
I am very excited to hear about that campaign!! Star Control 2 is a great setting, and it sounds like you've put a lot of work into mechanics specifically for it.
EDIT: Less work than you think, actually. Could probably fit it in half a dozen post-it notes. I'm sorta going out of the way trying to do as little "system hacking" as possible, and conveniently enough it fits with how ship damage is handled in SC2
FakeEDIT1.1: Another thing, to avoid dropping the players in space and tell them "yeah go wherever", I'm going to try to give them a more focused play. Well, sorta like missions. Not that I'll give missions, but they decide what to do
before leaving port, then run the whole thing as a scenario over 2-3 sessions, until the moment they finish whatever it is they set out to do (explore a specific sector, find a race, find a clear spindle, I dunno) and then they end up either back home or at some other docking point in the story. I hope that doesn't feel like a railroad, but I want "episodes" to have at least
some semblance of structure. No "going back to refuel" every 2 hours or whatever
Easier to run scenes that way I suppose. For example, give them a conflict scene, a talky scene, and a challenge scene in whatever order.