First off, im uncertain but I think the Vodyani are causing the pending issue.

1. they don't colonizes planets.

2. the planets they do have. is from minor factions.

3. once you wipe out their whole fleet or, the game starts pending. 

4. I think its cause ai is trying to move the ark. The ai doesn't know how to undock the ark.

6. you cant invade their capital while the ark is alive game crashes.

I played as the Vodyani once just to see why they don't do anything. and from I understand the ark is something like goa'uld they only have a fleet.