There are a few general opinions about the future.
Regarding Microsoft's involvement, some believe that they are not interested in continuing to produce a train simulator product at all. Others feel that Kuju is still the legal owner of the code for both MSTS and the incomplete MSTS 2, so Microsoft has to start over, and will come out with their own original code as MSTS 3.
Then, there is RailDriver, who bought PI Engineering (the makers of the professional TrainMaster Simulator software). They have announced that they are in the process of producing a home-consumer version of train simulator software, and are attempting to make it possible to import as much existing MSTS items & content as they can (routes, rolling-stock, etc). You can read their announcement here:
They also have a forum on train-sim.com:
http://www.train-sim.com/cgi/dcforum/dc ... =DCConfID1