I would much rather see MS Flight redesigned from scratch. If too much emphasis is placed on making it compatible with existing add-ons then it's more likely to end up becoming a bug filled mess.

It's also a great idea to move more towards flying in an online virtual environment. Real time weather, other users sharing one common airspace. Great possibilities for virtual airlines, air forces, simulated economics (FS Economy). The ability to automatically update airspace, nav data, ect. as it changes in the real world.