Experience is just added fluff since after a certain number of levels, you have all the modules you want upgraded to max, and don't need any more.
Really? I though I'd heard from several others that they didn't like how even in the endgame they never had enough to reach the stuff they wanted, and were trapped into their earlier choices due to a lack of XP to develop other branches. Perhaps I misunderstood, though.
I spent some time thinking about why I don't think the champions mesh well with the main game. I'm going to make some comparisons to another game that had hero units.
Warcraft 3 introduced a hero unit that could:
Gain levels (max 18)
Learn new skills
Resurrect after a brief wait
Do quests around the maps
The things that differ from AI War champions are:
There is a maximum level
You can choose the hero(s) you need but are stuck with that decision
Gains XP from normal enemies and from doing quests XP sources unlimited
Quests are not a separate map, and can be assisted by normal units
These things together allowed the hero units to mesh together in normal gameplay. I think too much effort was put into making champions their own separate thing that they don't mesh with the main campaign. They're like this sub unit that does it's thing, and then there really isn't any real conclusion to it other than everyone else got a bunch of nice stuff that can help out later.
I'm not trying to turn this game into Warcraft 3, but perhaps we can take a few lessons from it. Why not limit the levels of the champions to 12*hull level + 12. This makes maximum level 60. Then take XP from the mission, and put it in the main campaign only, in the form of killing shadow ships. This way the progression for champions is to help destroy clusters of ships bringing the shadow champions, and assisting homeworlders till they are of a level that they can deal with a nebula where they can learn new, and cool, abilities. The level limit still prevents them from leveling up everything they have at once even at the end.
Finally, rather than have all nebulas exposed at the start, have events that cause them to be discovered, possibly triggered by time and champion level. Upon discovery of an event, the champions have plenty of time to respond, but until they do, the nebula will remain hidden from view, as well as all other undiscovered nebula.
How does this sound? Level 60, which is the maximum you can achieve here is currently easily achievable if you game the system like we've learned how to. I've had champion levels of 78ish before. All it takes is dragging nebula missions out for as long as you can. It would also let you pick 10 modules potentially to fully level up per champion.