I wanted to throw up a post about minor issues I've noticed in the game.  Others feel free to add anything you find.

• Diplomacy ship for the Advent has no visual evidence of engines.
• Not really a big deal, but it really bugs me. 
• Some station techs result in no visual change of the station.
• It would be nice to be able to take a look at a station and be able to tell more about what it has implemented.  Things like trade docking bays and colony pods could make a visual change to the station like additional weapons do.  The armor texture could be changed to refelct armor upgrades too. 
• Weapon effects do not change when upgrade techs are researched.
• I'd really like to see the effects chnage as upgrades are researched.  If would make it visually evident what techs have been researched.  An armor texture change might be nice for armor techs too.  Same with shield techs.... 
• Special envirnmental effects have minimal effect on gameplay.
• I LOVE the idea of these, like the magnetic storm, but I wish they had more effect on the game.  Maybe more environmental effects would be added?  Maybe efects that span more than one location?  System wide?
• No visual effects for artifacts...
• It would be nice if some, if not all, artifacts had some kind of visual effect in game once found.  Something like a sparkle on diplomacy ships or a slightly different looking phase space jump effect.