I don't know where MS will end up, because every gen is basically random.
However, I do think they are in the best position out of the three.
Sony is in financial trouble and they have to support the PS Vita as well. It needs every support it can get, otherwise 3rd party publishers won't do anything for it either. Sony has a lot of homework to do. This might have an impact on the PS4 and the software support for it.
The Wii U is not exactly doing crazy numbers (not bad either btw) and the tech behind it is not new to anybody. They made a pretty big bet with the tablet controller and have to stick with it for about 5 years now. There still has to be the software that proves that this controller is more than a gimmick. Old ports won't do the trick. These are just as useful as standard DS3 games were to promote the PS Move.
MS biggest advantage this gen is that they are the first company in the videogame industry that understood to sell a service with the games. Xbox Live is so freaking huge compared to everything else. MS makes 1 billion USD per year just with the fees. This money is an undeniable advantage over the competition. The online business is head and shoulder above the competition. Sure PS+ is nice for you guys, but this is Sony playing catch-up. XBLA games, media functionality, streaming services with hundreds of Apps, Skype, smartglass and soon an even better interaction with every Windows 8 PC is just on another level. There are more than 40 million XBL users (not accounts) out there and this number will only increase till the next Xbox is released. This number is a year old already btw.
People are overestimating the games btw. 98% of the games are multiplat anyway. Halo, Gears, Fable, Forza, Kinect and a couple of new IPs from the newly built studios will do just fine. I think it will be all about the service in the future and that is where MS is leading the way.
I could be wrong though. As I said, a new gen is always random.