Here's a few:
How about an option to pause moon motion, but leave planetary motion on? After all, moons follow their planets around and have relatively tiny orbital diameters. It wouldn't break my suspension of disbelief any more than halting asteroids.
How about the ability to scrap PDCs, getting back some of the resources used to make them?
How about being able to chain up research in valid prerequisite order? I mean, to be able to say, up front, that you want to research, say, Mining Rate 500, then Mining Rate 600, then Mining Rate 720, etc, without having to use work arounds like top-queueing.
Actually not sure if this isn't in, but I haven't found it: How about ships being able to target their own current position/task group? For example, if I had a bunch of orbitals and tugs in the same Task Group, I would like to be able to select that in the location list, so that I could tractor the orbitals right from there.
Not so much a suggestion, as an inquiry: Is the database properly indexed? The other day at work, we had a major slowdown handling user requests, because there weren't proper indices in our database for the queries that the users were making. Adding them (an index each for every problematic query, with all the fields from the WHERE clause for that particular query) reduced request time by an order of magnitude.