Home is home
I've put some thought into this and realised a big part of what I'm missing is a home. Some place in the game where I feel everything started. In most games this is the main base. In Sins of a Solar Empire you basically build where you go and call no place home. There should be some sort of Galactic Council somewhere that basically runs the show and calls the shots.

Space is Huge
Another thing is the Space Lanes. The systems are too cluttered together and I think that's a part of why we don't get that I'm in a Huge Universe feeling. I wouldn't mind if Space Lanes were much longer, systems farther away and travelling between systems took much longer time. This way you would have to plan and maintain your attacks much more thorough. Every planet must count for something and be an important part of your Empire.

Variation is fun
All races doesn't have to have an equal amount of ships. The more variation that can be put into the races the better. I appreciate the problem is balancing everything but that's where mainstream separates unique.

The pilots are alive
How come the pilots aren't trying some evasive manouvering. It makes little sense that ships stop all engines and starts all bombarding. No, pilots would spin and try and evade enemy fire as well as trying to get in better position to get the enemy. Standing still doesn't make anyone feel alive. Keep formation if ordered, and avoid enemy fire!