I think that the larger issue is that companies, and perhaps even the masses in general, lack the imagination and wonder to really do/receive the space RTS sub-genre properly. It's so easy to do a historical game because you don't have to make many things up, but to make a good space RTS you need ships and races and lore and mechanics and sci-fi physics rules; it takes a metric ton of creativity before you even get to the asset creation and engine writing.
And when it comes to indies, I think they receive such little interest because they're the long shot. Like we've talked about before, they're at risk for real life to interrupt or halt development, and then you have a customer base left twisting in the wind. It's not like a ton of indies are made up of people who have worked for big studios previously and have experience not only in development but also the business aspect, and how many of them have made wise choices like you have?
On the one hand, but on the other it also frees you from the constraints of being locked into a given template because that's what people are used to. You can take HW2's three axis movement mechanic and combined that with Star Ruler's resource management mechanics and role in EAW/FOC's hard point mechanic if you wanted. The only thing stopping you is the question "does it blend together well?".
You have a lot more positive reviews than negative on Steam from what I can see and the negatives are largely from people who shouldn't be buying into EA games anyway. It's a lot like those one and two egg reviews on Newegg from people who bought a tier two managed switch or high end motherboard then write a bad review because they don't know how to navigate a command line interface or bios to properly set it up. It isn't the product or producer's fault the user isn't capable.
That said, all you can really do is keep working towards finishing. Along the way you're going to meet people who love, hate, enjoy, and are indifferent to SS and the most you can really hope for is to pick up meaningful feedback and discard the chaff.
I really like that new box on the top right, by the way. It should make tracking points of interest simpler.