Those are interesting suggestions for commander upgrades. Thanks for sharing those!
We'll see if we can discuss this with the design team for the future, in a couple of weeks. The usual biggest concern will be the effect of new combinations of bonuses on the balance of every ship in the game, so it might potentially need different limitations than what you listed.
As for the resource sinks - they still work and are still needed for everyone. For you guys they might seem like they don't do enough, but that's fine. We're also going to introduce new ones from time to time, at different levels so that each player has something to throw their resources at.