Gnome shell still includes the hierarchical application list that Gnome 2 did. The ordering of applications within any grouping is alphabetical, so I wouldn't have thought it made things more difficult than previously.
The problem with accessibility is that there's not any kind of "One size fits all" solution at all. It's a situation where two users may *require* diametrically opposed solutions. Accessibility is a fairly core part of the shell environment, and certain common accessibility features are now far easier to access and use than they were in previous releases. Right now there may well be some cases where earlier releases could be configured in ways that suit a given user's requirements while shell can't, and I'd hope that when people run into those cases we do end up with serious work going into fixing them.