When Joe Q took over as EIC Marvel had just come out of bankruptcy. 10 years (or so) later under his stewardship they were sold to Disney for $4 BILLION. That's how he'll be judged - not by story lines but by turning a dead company into a multi-billion dollar entertainment giant.
I wouldn't say this is the end of the Joe Q era - he is still the top man at Marvel creative-wise, it's just he overseas all media including comics, whereas Alonso will be just comics.
Judged: yes, I totally agree. But that's business. Remembered, ie by the comicbook fraternity: he'll probably score well as he's done more right than wrong. But, still, OMD...
Personally, I've loved way more than I've hated from the House of Ideas in the last decade, so well done JQ, I say.