Even though I'm far from an expert on Flash games and Flash portals, I think your three-tiered idea is very good. The backend sounds like it might be quite daunting to develop, and the biggest challenge, but if it worked like you described and your games are suffiently popular enough, I think it would work.
I know I recently visited Ninjakiwi's site just to try out some additional maps in Bloons Tower Defence 3. They weren't enough to keep me on the site, but the idea behind your first tier works.
Fostering a community (your second tier) is definitely the way to go when creating a portal, and maybe an "intelligent" flash games portal is a niche waiting to be filled.