Hey Dave,
I've done about 10 or 12 days at Thunderbolt, maybe 14 or so at Lightning and perhaps about the same at the Glen. Of the 2 NJMP tracks Thunderbolt is my least favorite though remember this is in the other car (Z06). I haven't had the Z06 at the Glen yet (and we are closing on our house on the 25th so no Kid's Day for us) though will be attending the Chin event on Labor Day Monday and the Tuesday after with some other NSX-ers if you or anyone else wants to join us (shameless plug).
Thunderbolt has an awkward turn, that is one that you just have to get through (Octopus). It is humorous to see everyone take a different line through it (this is in the advanced run groups so not like they don't know what they are doing), but it really slows the car down. I know you have the Supercharger so getting back up to speed before the front straight isn't as much as an issue as it would normally be for the NSX, but I prefer tracks that flow. Lightning flows. VIR flows. The Glen flows. Thunderbolt - doesn't. I know there are others who like Thunderbolt better than Lightning, but other other car drivers (higher horsepower) I've talked to have also mentioned their lack of fondness for Thunderbolt.
Since you've only had 3 events at the Glen then I'd suggest to build on what you have learned about tracking your car and the track itself so that you really get to feel in the groove so to speak. I think you've mentioned that you have been doing a lot of auto crossing, so going to a track you have some familiarity with I think would provide more opportunity to use your new skills. By going to a new track, you'll spend part of the first day just learning the new track. Well unless your ADD like me and then it will take you the entire day!
Perhaps you all would be able to finagle some time off to go to one of the best tracks in the nation (yes my opinion I know. Well, Paul Newman's opinion as well!) - VIR. It really is an awesome track and I love the Glen, but have to say, I love VIR even more. Plus they have some of the best track food I have ever eaten. Healthy - no. Good - omg yes! Homemade Biscuits for breakfast. True Pulled Pork Sandwiches for lunch. Plus, you'd get to drive with me again! What could be better!!!!
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Oh and not that this colored my opinion as I didn't like Thunderbolt prior to this, but my only HPDE incident was at Thunderbolt. In the rain. Going 30 mph. With my wheels straight.