Real-time space battle games are immensely hard to balance if there's any real options for multiple ships and customization in load-outs. Sometimes what's "good", becomes "uber-fantastic" in multiples. Not even a specific weapon, just types of weapons, or ones with unforeseen advantages or too low of a cost.
Then there's the "inverse squared" effect of firepower and range, where once a certain threshold of safe damage is reached, it becomes a gimme to win with it. But weapons usually get more damage, range, fire rate, or all three as you progress/unlock certain things. But where's the tipping point?
There's also the fighter-swarm effect, with similar thresholds, where the little autonomous buggers make it a disengagement effort for your main ships after you've reached a critical mass of fighters. Running away for dominance isn't sound as a fun strategy for winning.
There's also the "lots of cheap firepower" effect, where something in mass numbers removes any need for further research/progress, because a small lvl1 weapon is "good enough" even with damage and casualties taken into account, letting you just concentrate on repairs/numbers sustain without ever utilizing any of the other "funky weapons/shields/armours" that were so painstakingly created for you to discover.
You also don't want it to boil down to a very simplified rock-paper-scissors game, where no amount of forethought could prepare you for a particular battle unless you had prior knowledge of the enemy's makeup. And even then, you don't want it to be a counter-design chore, because that's not really a challenge, just some knowledge of game mechanics and a click-fest.
2d RT space battles are one of the hardest types of games to make. You sort of want a bit of all the above things, while not making any one or two of them overpowered. Options to focus in one of them and succeed, but options to spread out your types of weapons/ships as well, depending on play-style and playthrough.
Lots of options/add-ons and ship types is one way. But then there's also the "smeared across the RNG" effect to consider, where while you're making the best of what's offered to you, sometimes it feels that no matter what you did you never truly stood a chance.
Good luck guys. I could give an example or two of each downfall in the "genre", but at least you guys are trying to not leave them be, and are willing to take the occasional 1-star griper or poor comment simply to make the game better for all. Sometimes you have to listen to your players, but sometimes you have to be firm with your vision and make the best and most balanced game you can. Keep it up.
(ps. It'll never be balanced, but you've got to try your best).