Well oddly enough, Shockwave isn't all flash games. You can download full games from them as well, with an hour time limit, and then buy said game. They also offer a membership as well, to which if you play 9.95 a month and you can play their full selection. I don't know for sure how this translates into making money but that is what my wife has told me. As far as Yahoo, and RealArcade (Gamehouse now), I couldn't locate AI War in either of them. So they have either been pulled, or are not in their database to search for. Wife also mentioned a site called IWin.com that offer services like yahoo and such. I took a quick browse over there and noticed a couple bigger name games, like Puzzle quest 2, for instance, that is it's own game.
As far as your idea for a $6.99 micro-expansion for AI war, I think that would be fine by most of the loyal base. Most of us are understanding and care about the issues here at hand, and would love to help out if we could. If it is something that is feasible to do, then I'd say go for it. I'd be gladly to pick it up personally. I don't think your overmilking it, as the Charity with CoN can be marketed alot differently due to the fact that it is for a charity and not for your personal gain. Yes, it was an extra 4 bucks, but it went to somewhere good, and most people have no issue with donating a few bucks to a charity that will aid and help kids out. Marketing wise, that is how I would handle it if there were to be opposition that your releasing too many expansions.