I'm the friend Tridus mentioned above who got bored playing just the champion. I want to preface any feedback I give by saying that AI War is really not my kind of game, but that I play a lot of other niche games, so I understand and respect that a game can be "not for me." What might make things more fun for me may be to the detriment of the game for AI War's actual playerbase, so take this with a grain of salt. Additionally, while I did several different nebula events and unlocked another hull, my demo ran out just as I could've switched, so I only really got used to the human hull.
As Tridus said, playing the champion unit by itself bored me badly. What I don't enjoy about RTSes is dividing my attention between base management and military strategy. In a TBS I'm cool with doing both. In an RTS, one detracts or distracts from the other for me. The only RTS I've been able to sincerely enjoy is World in Conflict (Dawn of War might've worked if the writing weren't so bad) because it spared me that and let me focus on handling my units. Controlling a champion in AI War with Tridus managing the greater fleet at large seemed like a good bet, but what I needed wasn't simplicity so much as not bouncing all over. Playing the champion let me focus, but there was just way too little to do. Adjusting my ship loadout was absolutely fun. (Though I found the UI to be very player hostile, I greatly enjoyed getting to pick stuff for my champion unit.) Once I was actually playing, though, and had the options of "click a thing to shoot" and "project a shield sometimes," it didn't take long at all for me to be bored. I used to raid heal in MMOs, so I can enjoy the "whack-a-mole" of handling multiple incoming targets and deciding which needs to go down first, but when doing that always just amounts to click the priority, my attention isn't held.
In order for playing a champion to the exclusion of anything else to interest me, I need more than one ability. I need offensive and defensive abilities, both, though it's certainly fair for certain hulls to excel at one and be poor at the other. I do NOT need the champion units to be more powerful, just less monotonous to play. This can be accomplished by either a shared cooldown on abilities, or having all abilities spending from the same pool of shadow charge, or both as needed. This both gives me more variety in what I can do, and gives me tactical decisions to make. Will I better protect my friend's fleet by throwing up a shield, or by firing a barrage that lets him burn through an incoming wave faster? In a nebula event, do I speed things up and go on offense, or do I play it safe and defend the friendly AI controlled units? HOW do I go about this? Ideally, I'd also be making a choice as to which attack or defense to use.
As I said when I began, AI War's core gameplay isn't for me. It's entirely possible (probable?) that trying to make any aspect of it appealing to me as a gamer is not worth the potential upset to existing players. Tridus once suggested massive changes to Disgaea's core gameplay, and the mere idea nearly gave me the vapors. I respect that my interests may be detrimental to the game as its players love it--but here they are, nonetheless.
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