1) Cloaking ships/Anti-Cloaking ships (cloakers visible when attacking another ship only)
1a) This could work for structures too, I guess. Maybe a logistics structure could hide/cloak the fleet defending your planet, or conversely uncloak a cloaked ship that entered the warp well.
1b) An alternative to cloaking could be a Chameleon Device that could emulate an enemy ship type to facilitate a spy mission, or surprise attack.
Devs have already said that some form of stealth is in-game, for another race.
And I
really hated how spying was implemented in RA/RA2, lets not re-invent
that wheel, please.
4) Ability to trade/sell technology, among other things (similar to GalCiv)
Can't really happen. How do you trade techs between two seperate races, with different tech trees?
7) Advanced refinery ships/structures that could make Crystal and Metal over a period of time.
Whats the difference between this and the existing refinery system? Are you asking for the crystal/metal to come out of nowhere, rather than as raw ore from an asteroid (after teh asteroid mine goes kaput, that is).
10) A super tractor beam that could pull ships within range of Guass guns.
Gee, random much?

Actually, planetary defense overhaul has its own thread, or three, that you should post in. Most people tend to aggree that the gauss gun needs tweaking to be more effective, but its general role (close in defense) is exactly what it needs to be. Hangars (and a few other ideas) were thrown around as "grav well control" devices, while gauss cannons were effectively just point defense systems (defend a given point in the grav well).