#1 Con - NXT's identity will drastically change

Part of what appealed to people about NXT was that it wasn't RAW or SmackDown. It wasn't held in a huge arena and it wasn't given two or three hours with which to work. Those smaller crowds often provided a closer feeling between the wrestlers and the audience due to the size of the venue.
That independent-show feel is part of what made NXT its own entity. Smaller shows are more intimate and thus are often easier to connect to audiences. Most of the production for the yellow brand was primarily done at Full Sail University. If it isn't kept in Orlando, then part of that allure might get changed.
Another thing that worked extremely well on the yellow show was that a lot of the storytelling has been even. Storylines are usually carried out from start to finish. On the main roster, things sometimes start out one way but particular people lose interest and drop them entirely. Remember Daniel Bryan's career-altering announcement? It got dropped after weeks of hype. Matches for RAW and SmackDown have been announced a few days in advance only to change between being announced and the show itself.
Along with the close-knit feel of Full Sail is how most stars are received. For the most part, everyone was cheered or booed accordingly by the crowd. It was also refreshing to see stars like Breeze and Crews return to NXT and receive heroes' welcomes. They were a part of that brand's growth and have a special place in the hearts of NXT's fans. The small-feel show also made it feel like an independent show and one that was something completely different from the main roster.
By becoming a two-hour show overseen by McMahon, it will lose a lot of that endearing mystique that got fans to fall in love with it in the first place. It's still a WWE show under the WWE banner, but who it's run by and how it's run will certainly change once Vince is in control.