Joe Quesada's legacy will ultimately be how his utter repugnant attitude rubbed off on industry professionals who no longer even attempt to hide their contempt for the customer. What we have is this triumphalism and arrogance where pinheads like Joey Q, C.B. Cebulski, and Tom Broovert fiddle while the industry burns. I have nothing but disdain for Dan DiDio and how he runs DC Comics, but he at least has the good sense to keep is worst impulses in check when in public.
As for the continuity lock-out, man, I started buying Marvel books in the mid-90s when it was at its worst with the knotted X-Men lore and the ongoing train wreck that was the Clone Saga in the Spider-Man books. However, it was the X-Men and Spider-Man animated series that got me interested. They introduced me to the various characters and condensed classic stories like "Days of Future Past" and "The Dark Phoenix Saga" into something palatable for a preteen like me. As long as I could recognize characters like Cyclops, Wolverine, etc. and the art by Joe Madureira caught my eye, I didn't give a damn about continuity.
I'm embarrassed to admit that I liked Ultimate Marvel when it first came out because I was a teenaged edge-lord who thought Mark Millar's cynical take on the characters was the best thing ever. (He seemed to be obsessed with what brand of toilet paper the characters used.) However, I grew up and saw it for the schlock it truly was. It's rather unfortunate that Quesada and crew never emotionally matured past adolescence. Marvel itself has become like high school where they are analogous to the "mean girls" clique where they love to gloat that they are the ones running the asylum.
What they fail to realize is that the comics have been growing increasingly irrelevant with the ascendency of the Marvel Cinematic Universe. While it is true that the MCU strip mines the comic lore for ideas to regurgitate for general audiences, fewer people recognize the comics as the "prime" canon and the MCU has--in fact--influenced the comics more than the other way around in recent years. By all means, they can sneer and gloat all they want, but it is exceedingly rare to even see comics on magazine racks at any retail outlet. Their shitty attitudes are driving long time fans away and their shittier business practices are forcing comic stores to close or change their business model because they can't sell the shoddy merchandise.
When the comics industry finally goes tits up, I will point the finger of blame squarely at Joe Quesada. The man who killed Marvel.