Would it not make more sense to let Space Stations be "constuctable" by Colonies with out the need for a construction facility?
You cannot build bases without a Space Yard. That is hard-coded.
On another note. Is there a scanner that lets you see what's on a planet/colony from space?i.e.Facilities/Troops etc? 
I seem to remember having this ability in the Original SEIV game, but it's so long since I've bothered with the non B5Mod that I've forgotten? 
No. You have to attack a planet to see what's on it.
Re: Fighters. Does anyone have any pull with MM? I think it would be cool 
if fighters could use Jump Gates/Warp Points...
MM listens to the masses.
If enough people request a feature (that isn't impossible to do within the game code), he usually adds it to the game.