I don't really agree with this. From what scenarios I've played (the ones you are describing), it plays a lot like a game of anti-DotA/LoL. You snipe off enemy ships and escort your fleet to the enemy bases, for a big attack on it, rather than killing off enemy creeps to get strong enough to team up with other champions and go for the towers. I haven't even played with abilities, and I had a fairly easy time getting a grasp of how it worked, and I felt significant. If I didn't kill off waves of enemy ships, then my side's ships would be outmaneuvered or outgunned, or at very least, slowly picked off so that they don't stand a chance against the starbases.
I do understand the idea of not feeling particularly involved, however. I mean, it's sorta YOUR scenario, you should be able to directly shift the flow of the battle by being particularly powerful, or at least having reasonable control of the battlefield. As a player, I didn't really ever feel like I had much control over what was happening, but the support I provided with my champion is without a doubt invaluable.
What if you were named a general, and were able to control the neutral-ally ships in the nebula? That might allow the player to at least feel more involved in what was going on. Before really thinking about that though, is it really a problem that you're just a strong guy supporting the other faction's cause? I don't think it's actually a big deal.