I thought the article had some good points! Although one should perhaps not be too quick on judging sidescrollers, etc since that is more of an interface choice than gameplay (as soon as u start hopping on platforms, etc, you go down more well defined path though). Guess that author implied that though.
In the end Braid is not better than Mario. Not even as a metaphor.
For me Braid did not feel as a step closer towards art in games (whatever that means...). I really liked the game and most of all its esthetically design such as the vague texts, the visuals, music etc. Was really a joy to play and experience. But I did not feel like it gave any deeper meaning any more than Mario did.
Whenever people remake platformers or similar, then it is almost always a reflection on the game mechanics. I have never seen an example where it is a reflection connected to real life. In Watchmen, the superheros are put in a real world context and ll kinds of implications are worked out from there. If platformers where to bring the games in new direction, they should do something similar. But as you say Michael, then you will probably have to abandon the qualities of the old game and this is sacrifice few (none?) wants to make.