So you want to write a mod or do you just want to have suggestions on which ones to play?
Modding usually means that you make a mod but it seems like you just want to play them.
Most mods are good in their own way, most of them add new factions and star systems.
There are more complex ones that add new features or completely change SS, Total Conversions those are called.
I can suggest Uomoz' Sector for a start, it is a verygood mod collection which adds new features as well, probably the closest thing to what SS might become one day.
Adding some faction mods together with Exerelin is a lot of fun, basically it is a huge multi front war with the goal of conquering star systems. It's also very much a sandbox like gameplay.
If you want to try out something completely different try Ironclads or Vacuum. (It's still SS but with more clearly defined goals and a lot of custom features and balance in case of Vacuum)
I hope that might help!
PS: If you like Zerg or Tyranids try my mod, Biomancy Genetic Engineering. It is very different although it's just a faction mod, see for yourself if you like.