Moon Girl and Ms. Marvel actually are in floppies first; I don't know if they're just doing so well in floppies that it didn't matter (possible, they are really good books that got a lot of good press early on) or if the publishers decided to take a chance and push through until they hit the trade markets, because they knew that books for younger audiences do really well in trade. But I'm thinking more like the graphic novels published by Scholastic and First Second and the manga-only publishers that sell mostly through booksellers and don't care much about the comics-only market. (DC has been trying to find its place in that market for the last decade or so, and I think they finally managed with the Superhero Girls line; Marvel keeps dipping its toes in and out with things like Marvel Adventures and its cartoon tie-ins.)

I suspect what will happen is that most of the comic book stores will go out of business or shift to mostly gaming/merch stores, floppies will become even more of serious collector's items only, and nearly everything will shift to trades sold through book distributors. But I dunno - that would be a huge change not just in how the comics are sold, but how the stories are told. Maybe some hero will come out of the woodwork and save the direct serial market! (Although if everything does shift to trades, I suspect you will also start to see skinnier and skinnier trades coming out more and more often until many trades are just more expensive floppies....)

(Comixology and ilk are kind of running alongside the rest of the market; but somehow ecomics don't seem to have become as big a thing as a lot of people were hoping. Maybe because they don't factor in e-comics sales either when deciding whether to renew major-publisher books....but I think a collapse of Diamond's system would also lead to more high-budget electronic-native comics, too.)