I agree with you completely, I think we are saying the same thing.
The charter NE schools are historically weaker in football (due to pro markets, less emphasis on HS football, etc...). Why does not really matter...they just are but that does not mean NE football should not be exciting. Unfortunately, the NE schools sold each other out without regards to how rivalries effect programs.
Syracuse, BC, and Rutgers are more exciting programs and benefits when they plays Uconn. By not playing Uconn and trying to kill Uconn's athletics they are hurting themselves. While other regions of the country may not care, for the fans in the NE, it is a big deal when the regional teams play. The fan bases of both teams attend the game and the excitement generated far exceeds the talent of the teams. This excitement translated into ticket sales,TV revenues, and money.
The "big" football schools know this and this is why they have fought so hard to preserve there historic rivalries. One of the main reasons the Big12 has stated for not expanding is they want to preserve yearly rivalries like Texas-Oklahoma.
When conference realignment first occurred plenty of team who are "hated rivals" fought to stay together (Uva/Va Tech, Okla/OSU, etc..) While some of that may be political, a large portion of it is the understanding the "big games" are as much about rivalries as rankings. Before this year Michigan football had been struggling but the OSU/Michigan fan base was still fired up to play the game.
As a Uconn fan I watch every Uconn football and basketball game. I cheer for my team but I do not feel the excitement like when Uconn was in the BE. Houston may be a better football than Syracuse but I'd still get more excited to play Syracuse. It not about ranking...it is more about shared history.
The proof is in the pudding and BC is the best example. BC used to have a very competitive sports program but it broke off its historic rivarlies and tried to go it alone. Now BCs sports program are a shell of their former self and most teams in the ACC have no particular passion when they play BC. My predication is when Uconn-BC play in football it will be one of the best attended games of the years for both BC/Uconn. Neither team may be ranked but it will be the game both fan bases circle on their calendar.
It is just sad the NE schools sold their identify for a few extra bucks...