I remember using bitlbee with Skype. The problem was I had to keep the official Skype client running. I believe it was the same for pidgin's Skype plugin?
I don't know about XMPP transports specifically but this is mostly a frontend app change and not the backend. The MSN/Messenger servers are still the core of all of the messaging platforms and will stay in operation.
That's a good question. MS started to move in the right direction with XMPP support, even though they didn't get up to supporting federation. If that will be dropped - it would be just another proliferation of the isolated IM networks.
I'd love to have the same for Skype, but last time I checked, Skype had them all (all unofficial clients) banned...