This new site is super-awesome and challenging, but a great thing about the hexagonal grid in "A Regular Crossword" was that each hexagon was constrained by three intersecting regular expressions rather than two. That meant that the constraints could be trickier or vaguer in some ways, and comparatively more dependent on the sequence of elements within a regular expression rather than on the process of elimination between two intersecting sets.
(Just so it's not credited to MIT in general; each year's Mystery Hunt is written by a specific puzzle team, and indeed each puzzle is written by specific puzzlers!)