I agree, it was flawed. And it was not going to win a Superbowl.
But that's irrelevant. It was good enough to back into the playoffs and maybe win a game there with a great defense. We had the #1 rushing attack in the NFL by a lot. There was enough salvageable there to not blow it up. Do I think TT was the long-term answer? No. However, if the Bills were gearing up for a 2017 playoff push, which they are (a mistake but an understandable one), the move is not to bandaid the defense which sucked and rip out the whole offense. You put the best team possible forward. They are going to make the fatal mistake of taking a day 3 QB, keeping TT and changing his system. And I don't think anyone can argue that TT is at his most effective throwing the ball 15 times, and helping McCoy and TD Mike find wide open lanes because he's a threat to run.
This is nothing new with the Bills. They did it 2014. Our owners and GM fundamentally do not the importance of continuity when things are okay. They have proved it again and again.
Personally, I don't think it much matters because the 2014 defense is dead and gone and this group won't play to that level in 2 years or so. But if they revert to 2014 form with draft adds and FA's, which I think Whaley is banking on, and your goal is to make the playoffs, you do not destroy an offense top 10 in points scored. And that's not just TT. You can ditch him, get a guy like Watson, Romo, Rivers, and still keep the O together. But ditching the OC and his system and the QB is a recipe for disaster.
TL;DR You change schemes, coaches and key players drastically when units SUCK, not when they have numerous tangible positives.