Issues:
- You can't have an orphaned shipyard - the game won't let you proceed - you are forced to find a sponsor. You should be able to have a shipyard that's inactive and/or orphaned.
- United Planets Council ALWAYS adopts my proposals - is this WAD? (Working As Designed)
- AI always categorically rejects my Alliance and even Non-Aggression treaties no matter how much I bribe them or how much they like me - is this WAD?
- Idle colony bug - game won't let me proceed - can't see what to build or upgrade in the colony (it's maxed out with buildings) in order to get past this
- I have 2 civ capitals! (Altaria and Easluna)
Suggestions:
- Useful to have a "don't colonize in my ZOC" treaty rather than just relying on the UP Council resolution, which is infrequent and doesn't last
- Like in the Total War series, how about having a "declare war on civ X" diplomatic option to ask your fellow civs? This might do away with some of the point of Alliances, I admit, but they seem impossible to obtain currently anyway and should you always need to be allied to a civ to get it to go to war with someone else? - a decent bribe or some techs etc. might suffice 
I have never got an Alliance, despite my best efforts, so I don't know how your ally deals with your enemies.
* This is a bloody good game in its current state and the developers are geniuses.