I have no problem with the take that he's a franchise QB, but he was not our franchise's QB. He's not a good fit for O'Brien's system. (He probably would be great in Kubiak's bootleg-happy WCO, though).
Read this
analysis of Greg Olson, the Jaguars OC. He adapts his scheme to fit the players he has on hand. This is a key paragraph comparing the previous OC and Olson:
"In the first two years of the new regime, the Jaguars employed Jedd Fisch as their offensive coordinator with a zone-blocking scheme and a quick pass offense that revolved around getting the ball out quickly, precision short-passing and bubble screens. Lots and lots of bubble screens. That seemed to fit the likes of Chad Henne and Blaine Gabbert at the time, but when the Jaguars drafted Blake Bortles, many wondered how the offense would change, because all of those things were things Bortles was not good at.
Fisch ended up getting fired, because it didn’t work. At all. The Jaguars offense in 2014 was atrocious.
Enter Greg Olson, the chameleon, and suddenly the Jaguars have an explosive offense. Sure, he gets the benefit of a lot of these younger players having been bled in the NFL for a season and are in the middle of their development, but Olson has put them in positions to succeed. No longer are the Jaguars operating a quick passing game with bubble screens, but instead they lean towards Bortles strengths. The offense rolls and moves the pocket. The offense attacks the intermediate area of the field and they’re aggressive down the field. All things that Bortles is good at."
The blue bolded is pretty much describing the NE system that O'Brien uses. Advanced pre-snap reads and quick release after the snap. The QB needs to know where he plans to throw the ball before its snapped. O'Brien doesn't do bootlegs much. He wants a pocket passer with the brain of a field general.
The red bolded is Olson's current scheme, which is basically a version of the zone-read. This obviously works well for Bortles.
If O'Brien had picked Bortles, they would have struggled with each other. It is clear that O'Brien is looking for QBs to fit his scheme, and he's not a coach that is going to change his scheme to fit the player (unless it's adapting to dire situations like starting Keenum, Weeden, Yates, due to injuries).