Still processing all of this.
Pegula hired/retained/fired two green GMs (Whaley and Murray) who were, essentially, scouting experts, not team-builders or CEOs. He gave those GMs undefined roles and thrust coaches on them who were not qualified and with whom they did not get along. These were recipes for failure. So in both instances, the firings seem a bit unfair.
That all said, wrt Whaley, this almost had to happen. Even though he may have been set up to fail, he did not do himself many favors by butting heads with two successive coaching staffs and by taking the wrong risks at the wrong time. Some of it was bad luck (injuries to Sammy and Ragland) and some of it was just plain ill-advised. To me, it wasn't the QB issue that doomed him, it was coming out of last year's draft with absolutely NO HELP for the 2016 roster. Yes there was bad luck involved but it was also not the year to spend two picks on players known to be injured (Listenbee and Shaq). Getting three players poached by the Patriots in two years (and having to fill those holes through the draft) was also a black mark on his tenure. And I'll say it again, regardless of whose fault it was, the lack of short-term and longer-term strategic planning was clear to outside observers.
Time will tell if they've now got it right. Pegula may be a kinder version of Dan Snyder or he may finally have learned how to run a sports franchise. We'll just have to see.
EDIT: I'll add that horizontal power structures, which Pegula professes to prefer, lend themselves to political infighting. We've seen evidence of that with both the Sabres and Bills (LaFontaine; Brandon). Pegula needs to get that sh- under control and weed out the snakes or neither franchise is going anywhere.