Theres no denying, our industry has been decimated. There may well be some long term structural changes on its way and the 787/350 have opened up the possibility of more point to point services. However, to suggest that the 'hub & spoke' model is dead is somewhat premature at best. I think we need to be careful what we wish for here. All the heavies we all love to see at MAN, SQ, EK, QR, EY, TK etc are all "cross contaminating shuttles". Furthermore, if it wasn't for the hub & spoke model, I doubt we would see (for example) QR or SQ and a much thinner schedule from the likes of KL and LH.
You mention Virgin/Delta which again rely upon connections, certainly on ATL and JFK and I think the success of EI will probably rely to an extent on some kind of connectivity stateside.
Short term, there may well be scope to formulate some sort of quasi-charter programme but I would say that is best driven by the tour operators.