No idea if any of these things are in development. Some of them could be done as a small DLC or part of a patch, others will need a full blown expansion.
1. More ideologies - Taking inspiration from the civ traits. This would, if done right, add even more flavour to the game.
2. A good espionage system complete with improvements and possibly spies that you can move on the map in the form of a ship with a special module, and capture, of course.
3. The ability to eventually terraform over (a long) time dead rocky worlds. Very late game tech and very expensive to do. Possibly using starbase modules?
4. In game Custom Civ Editor having many more options so we can make custom home systems (with a points system like the traits), ship styles and such from within the game.
5. The ability to designate which particular Civ will start in a particular system in the map editor.
6. An in game logo creator made with elements from existing logos and with a colour slider.
7. Ability to upload mods to steam and use them in multiplayer. Uploading mods to steam would probably require some kind of 'does it work?' checker thing, but allowing their use in multiplayer I think is quite a biggy.
8. More domestic stuff to do during those periods of peace: Political Parties and elections, a civil war mechanic - both would tie in nicely with espionage, crime and laws, etc. Ruling parties and laws could affect dimplomacy.
9. A slighlty more complex and involved planetary invasion system. Doesn't have to be RTS, but just more than a button click.
10. Remove wormholes from anomalies, disable them on smaller map sizes, and make them map objects. Have some permanent, some temporary (say between 2 and 5 turns) and others with no exit.