I would like to see a full universe with an x y and z axis. Animate our ship so it can fly around the system 1 square at a time. Instead of scanning by a chance system, have a scan that works by location. (ex. if you are at coord 10023, 593, 9382 and your scan power is 1000, you would be able to find another system that is at 10109, 700, 8900.)

There was an old game called Fatelords that used this type of universe and it was awesome. It added a lot of depth to the gameplay.

Also, it would be nice if the focus was on planets more than your main ship. I would much rather build my planets, than focus on my capital ship. It would also be nice to build other ships for specific tasks.

Probe for scanning
Fighters for taking down bigger ships
Bomber for planets
Cruiser for defense and ship to ship battles
Pirate Class ship that raids other ships cargo
Colony ship that colonizes planets
Storage ship for storing mass amounts of cargo

etc...

this isnt galactic civilizations... but i see what your saying. i dont think it would be good to controll millions of ships (because thats what it would come to once your level 700) but i would enjoy a special module or something that are fighter planes, and either add a bonus when under attack, or add a bonus when attacking, where the player chooses wether or not they want defensive or offensive fighters to be docked in their hanger.

as for the grid, i liked the grid idea when it comes to the daily reward, but i think it would be annoying if all your planets where from a specific area, and then a person 300 levels above you decides to do a scanning blitz in the same place and takes all your good planets.

The sector scan was suggested before, along with support ships.

You are suggesting to make this game entirely different.
The game you want have already been made, it's call unification wars.

is that game any good?

I enjoyed it when I played, but it ate up a lot of my time, so I stopped.