I'm just going to go through and comment on the suggestions in no real order...
Ship captiains was requested in the "idea gathering" phase of SEIVs development, but was dropped because (I think) it was too complicated to keep track of a captain for every ship.
The "Asteroids" environment in combat... it's eye candy, and doesn't add or detract from the game. There are other things that have priority over this.
Larger stars... ok.
Unmanned probes == Drones. They're supposed to be put in, hasn't happened yet (pretty sure I still have the drone pictures in my races' directories, and I haven't heard anything about drones from MM).
About missiles being deadly... they're only deadly when you're caught with your pants down and don't have any PDC. One or two on every ship effectively nullifies the offensive potential of ships that use missiles.
Break up unit Groups... Yes, please.
Computer control... just check the little box
Ummm... the comment about active sensors in cloak... explain? I have no idea what you meant by that.
Pseudo-real time play... I'm assuming that you mean a modification of simultaneous turns, where each turn has 30 "days". The days would pass after a set amount of time, so things go on while you give different orders... Not too high on my wishlist, but it would be interesting to see. It would bring in a whole bunch of new bugs, bringing in a new "turn"-style (MM had a hard enough time getting Simultaneous to work right), so it should wait until other issues are resolved.
Starting techs... Yes, please.
Exact Computer Numbers... Yes, please.
Turn off QReactor... I think you can turn it off already, if not, ok.
I've already voiced the major flaw with the no warp point facility... this effectively cripples the AIs ability to attack human players once this facility is built. Close all warp points in system, AI can't get in, you have ships and SYs outside of core systems that can attack AI, AI can only attack the attacking forces, can't affect the economy of the humans. Unbalancing.
Build on all planets... I usually have most of my planets already building stuff, so if I use this, the build on troops/whatever would be delayed, and by that time the unit would probably be obsolete...
All planets start in one system... you can already do this, just select one starting planet
Or, with the map editor, you can set a starting point where all the planets are in a single system.
Allied play... cool.
Bribe... I don't think the AI can comprehend the fine art of bribery... I mean, they can't comprehend lots of things already