VirGen is a good deck (if you can play it - it's tougher than TDK), but for BRs, it looks like it's overhyped enough that decks without a good VirGen matchup are going to not appear as much. VirGen still loses to TDK most of the time, which is very bad, as the Thundurus/Deoxys/Lugia tins means TDK will only be increasing in popularity.
There will be VirGen at BRs. It's expensive enough that it will be rarer than TDK and most likely Blastoise as well, but I expect it to be present in most metagames.