There is a discussion about this in the Universe forum, I think we need to have one in the Fallout Series forum so it could be a bit more official, if you know what I mean.
As we all know, Bethesda really doesn't like setting canon endings as evidenced by the Warp in the West. While in the Elder Scrolls series such a thing can be forgiven as a one-time thing, especially since you had little reason to go with most of the endings in Daggerfall (seriously why would you give the Mantella to any of the Bay kings, Mannimarco or Gortworg?), but the Fallout series and some of their own stuff now are a lot different. With the presence of the Imperials vs. Stormcloacks, the Pitt and Paarthurnax it is quite clear that either Bethesda will have to defeat their attitude toward canon endings or they will be a step closer to becoming laughingstocks on the level of Bioware.
So the question is this: to what extent should they set canon endings and to which games? It is a no-brainer that the FO3 canon ending should be the ultimate good ending, but the Pitt and NV are different. My opinion is that they should not set canon endings for NV and Tactics, only to the East Coast stuff. They can have subtle references to NV, just like they had to Tactics in FO3, but setting a canon for NV, especially if it's a boring or bad one (like NCR or Legion), is just going to give off the same vibe as Oasis or MZ (the "our franchise now, you can svck my dike" vibe). Then there is the issue of what should be retconned, declared non-canon or just simply explained away. MZ should be declared non-canon (it pretty much already is); Oasis should be too, even though I was never really a fan of Harold and what they wanted to do with him in VB is worse than Oasis, imo; Vault 87 and the no plant-life plotholes should be explained away in a logical way (there are explanations that filled in those plotholes, but also created even bigger ones). The "explaining away" will be made a lot easier with the Institute but only if they get the Institute to be plausible.