Yes, champions do give me a sense of "hero units". I guess what I'm thinking would involve more personality, but champion would be and easy way to kick it off. A personality or several that I can cheer for as we plunge ahead. Exploring the possibilities is definitely something that intrigues me.
Hum... it's true that champions lack that "heroic" feel. They seem more like expandable modular ships than truly heroic units to me.
In gameplay terms, it's the lack of unique abilities that make the champions look like all other units. They have shadow power-energy, but we only have one or two abilities per ship. More abilities would make them more distinct... but from a development perspective, they're a time-hole.
One thought I have would be for heroes to be more things to capture/hack, where they are a sort of galatic-wide/fleet-wide/system-wide upgrade.
That take it away from the champions though...
Well, I could see "heroes" modules being given to players to put on their champions, with using of the achievement system to make the heroes unlockable through doing some achievement within a game. (Like mini-achievement. reclaiming a a few hundred/thousands AI ships within a game would give a "hero" giving a bonus to reclaiming for the rest of the game.)
Regarding lore, making heroes back-story would be a task best given to the community. There are a few people here that are undoubtedly willing to create some interesting persona, and it would lift the time eaten for that particular task from the developers.
Dunno. I'd really like for champions to be more heroic rather than convenient raiding-scout-kamikaze, but anything like warcraft3 or RPG with heroes having many unique abilities would consume far too much development time for AI war.
A pool of more generic abilities, that could later be recycled for the AI use, might be easier... but not necessarily easy.