We have to accept the fact that not everyone likes the same thing and that goes for "messy" as much as anything else. Some folks want their theatre delivered in a tidy package. This is true of plays just as much as musicals: the well-made linear play. Others are stimulated by the "mess." There is definitely a constituency on this board for what's un-messy, traditional, unrevised, etc. [I think some of this is fed by a white hetero patriarchal sensibility but that's beside the point here.] My impression (which informs my grain of salt) is that this constituency has grown here over time (in percentage if perhaps not absolute terms) even as (perhaps because?) it has shrunk in other precincts.
Two final observations. First (and this is one we should never lose sight of), Hamlet is the greatest play written in the English language and is also one of the messiest. How many words have been written trying to decipher its meaning? Second, it's important to remember that the Pulitzer Prize is simply a consensus of a small (not especially representative) group of people about what play they liked best in a given year. I think a more useful metric for ranking plays would focus on importance. Even among Rent's detractors, for instance, it's hard to imagine that there is a reasonable argument that it was not important.