Zekrom now posses a huge threat to PrimeTime... On the bright side, if you hit late game, playing N and KOing something with a lot of energy could end their stream of attacks. Zone now needs 3 energy to KO Zekrom, which actually makes all of the difference. Yanmega also doesn't beat out Tornadus like it used to either. I have thought about Terrakion but I'm not positive.
The Tyram match up hasn't been effected much at all with NV. If anything, N makes the match up better for PrimeTime than it used to be.