Soviet Heavy said:
The Brotherhood of Steel war with the NCR, Joshua Graham's pre Burned Man days, and Caesar's Legion were all set to appear in the game. So parts of Van Buren's plot are still canon.
Except ALL of those things are heavily modified, and differ in many ways, from the original design in Van Buren. Van buren is not canon, for the simple reason that New Vegas doesnt support it.
Victor Presper, the whole BOMB satellite, the prison controlled by an AI, it never existed.
All you have to do is look at how Joshua was in New Vegas, and how he was going to be in Van Buren to see that they are wildly different.
http://fallout.wikia.com/wiki/Joshua_Graham#Van_Buren
That is why the wiki states "The following is based on Van Buren and has not been confirmed by canon sources."
There is a very large difference between being canon, and having bits and pieces be altered and adapted into canon. Van Buren is the latter, not the former.