That's a good point; we've thought about it. As a knee-jerk reaction, the idea doesn't sit well with us because it's a less-than-ideal experience. Users don't want to sit through or be saturated with ads, but I guess it does come with the "web-based game" territory.
Have a look into http://flashgamelicense.com if you haven't already. If you have a quality game, you can actually end up with a bit of a bidding war going on between potential licensees, and most deals allow you to sell again to other sites after an exclusivity period. Each of our Pretender games so far (http://launchingpadgames.com/games/the-pretender-trilogy/) has earned in the high four-figures, with zero in-game advertising except for fairly tasteful co-branding from the sponsoring sites.
I guess I don't really see it as an either/or scenario. Why not leave the app on Chrome app store and also put it into circulation on Kongregate or wherever?
