A Chorus Line was nominated because it is a faithful adaptation of a well-loved, American musical, and it is introspective and tells a story about those who create stage entertainment. This production was not designed to be innovative or to rethink the material, it was designed to pay homage to the original and allow a new generation of theatregoers to see it.
I am the type who would have preferred the creative team take a stab at taking a new approach to the material. But maybe this just wasn't possible--maybe Michael Bennett's direction is considered too untouchable in the same way that Jerome Robbins' choreography in West Side Story is not something choreographers typically mess with. In any event, reinvention certainly wasn't going to happen when the creative team consisted of those associated with the original production.
As for the Tony noms, it was a no-brainer nominee given the weakness of the field. I mean who else would have been nominated - the down-sized Les Miz that just closed yesterday? But the only way ACL wins is if the voters rely solely on admiration for the original material, as opposed to admiration for this particular production. Company is far more inventive, interesting, moving and theatrical. I have no problem with "faithful" revivals, but when it comes time to pick out award winners, invention ought to count for something.
"This is wanting something, this is reaching for it,
This is wishing that a moment would arrive.
This is taking chances, this is almost touching, what the beauty is." --The Light in the Piazza