One thing I love about Sins that I feel other RTS's need to pay attention to is how low-management the economy is. Structures and planetary upgrades require no further oversight once constructed, workers are automated and replaced automatically so you only need to manage them when it's relevant, and unit construction is automatically balanced between factories in a gravity well. This sheds a lot of micromanagement inherent in the genre while losing practically no strategic depth in the process. I feel that any Sins 2 should strive to maintain that streamlined elegance.
One thing I think didn't work out too well is stars. Having exactly one way in and out of a solar system and having all those launching points be connected to each other just lead to massive fleets being stationed on stars. There is exactly one front-line, harassment is difficult since large forces of carriers can easily intercept smaller forces, and the entire game hinges on control of these handful of gravity wells leaving the rest of the map layout somewhat redundant. Multistar games tend to be long, boring, and formulaic compared to single-star games which often feature multiple fronts separated by vast distances. A relatively simple solution, which is seen in some premade maps, is to connect solar systems with interplanetary phase lanes to reduce the focus on the stars as the sole junctions.