first i'd like to say i am perhaps being over critical, i think it's a fantastic library (framework). i just realize how intensely better it could be. my biggest pet peeve is that it is indeed a framework, not a library. i really wish they had taken a route similar to jquery ui- and not try to force so much on you. this is for another post though.... as far as your question goes:
i don't think it's true to say scrollview and transitions are a lack of hardware support. again, on my iphone 3gs and 4s the google+ app is flawless in both of these areas. jquery mobile is subpar. the scrollview is obviously forgivable since it is still experimental. for what it's worth, i still think it's a far superior choice to iscroll.
the first issue i'll bring up is their fixed header and footer support. i think it's a decent solution for the tools they have available, but i'd never use it myself with it's current behavior. i do realize this is probably a consequence of scrollview support though.
another problem they've yet to solve is url bars dropping down while navigation. i understand given the circumstances, this is a difficult problem to solve without going against jqm's principles.
i am also not particularly fond of how their active states trigger on scroll, this is obviously not desirable.
my argument is not that there is much that is missing from jquery mobile, like i said i have a lot of faith in the project. stuff like url bars, active states, and page transitions may only be the last 10%- but that last 10% is crucial for the final polish of a real release.