As its been mentioned, with the guys its not that big an issue - but with the girls, a lot of the top runners are on NTN contending teams:
Check out Tullyrunners.com:
The top 12 at the moment
1 Hannah Davidson 12 02-AA Saratoga
2 Sam Roecker 11 02-A Burnt Hills
3 Hannah Luber 10 03-AA FM
4 Jillian King 12 02-A Scotia-Glenville
5 Kathryn Buchan 11 03-AA FM
6 Mary Kate Champagne 12 07-D Seton Catholic
7 Molly Pezzulo 9 02-A Burnt Hills
8 Tori Pennings 12 09-AA Warwick
9 Caitlin Lane 12 02-C Greenwich
10 Jocelyn Richards 12 03-AA FM
11 Catherine Lusardi 12 06-B East Aurora
12 Shelby Greany 11 01-AA Suffern
Now, considering two time finalist Shelby Greany is 12th and running fairly well, all the girls in this group could potentially contend. The majority of them are coming from the teams - 'toga, greenwich, FM, East Aurora, Burnt Hills - all top teams. Davidson has already made three trips to FL. Lane has made two. Davidson and Roecker in particular are top FL contenders, and both of them are crucial to their respective team scoring. (Toga is improving slightly, but they cannot beat Burnt Hills without Davidson.)
The net effect is that some of them won't run FL NE (diluting that meet.)
The net effect of having to "peak" for a qualifier is that some teams won't run feds (a move Hilton made the year they won, and a move that dilutes the competition.)
What IS Nike trying to accomplish?
If you ask me, it would make more sense to run the Fed race and have an open NTN race following that one just so that all teams can participate. Of course, this could lead to sanctioning issues so perhaps that isn't any good either. Regardless, bear in mind that NY has dominated NTN in the team competition on the girl's side the past couple years (though at FL the NY girls have not had a good year since '02!) which makes me lean towards the idea that this is a bad, bad, move.