The glaring omissions in my book are Annaleigh Ashford for Sylvia, Tuck (set design, choreography, music...), Daddy Long Legs for music/lyrics and acting and Jennifer Simard for Disaster, Blackbird (I do wonder now if it wasn't eligible).
Also noting that Ben Platt didn't get nominated, and neither did Audra (or Shuffle in any acting categories).
Glad to see Shuffle went into NEW Musical, not revival, but shocked it got nominated. The show was still a mess when I saw it a week ago... Bright Star and American Psycho on the other hand got so many noms in other categories but then didn't get in for Best Musical, which is just weird.