Conference meets will become irrelevant for those who cannot be sure of their spot in the top 96 in each event. No point in wasting a 10k, 5k, or even a 1500m effort when so much is on the line. On the bright side there will never again be those regional qualifiers who can't break 15, 9:30, or 3:55.
For reference here are the 96th place times in distance events in 2008, and the number of regional qualifiers based on time in each event:
800: ? (88th was 1:50.38)
1500: 3:46.51 (134)
Steeple: 9:04.89 (111)
5k: 14:11.08 (100)
10k: ? (26 ran at NCAA's)
Of course these times are irrelevant since the lack of time standards will change everything.
It will be interesting to see how NCAA coaches game the system. Last-chance meets will have more on the line (imagine being ranked 92nd in the last weekend to qualify with a time from Stanford). College coaches will also have an incentive to make sure everyone not on their team runs slow. I can't imagine how that will play out, but there will probably be some interesting gaming of the system that nobody could have foreseen (For instance it will be imperative that your athlete gets into the fast section, but also that someone else's athlete is kept in the slow section).
As always, most of the qualifiers in the distance events will come from Mt. Sac and Stanford. And we're gonna see a couple huge championship 10k's, or 4 worthless semi-final 10k's. There will be a discrepancy between the two regions that in some events will seem extremely unfair.