Yes, there is an unspoken "no more than 2 nominees per show" (with some exceptions), which explains a lot of the omissions. I am surprised, though, by the omissions of Patrick Page, Spencer Kayden, and Danny Burstein, all of whom I think will get a Tony nomination.
In addition to the weird thing that Arianda and Shamos are getting re-nominated for the same role, the productions of Other Desert Cities, Clybourne Park, and Venus of Fur are also re-nominated for Distinguished Production of a Play, which seems strange (particularly for Clybourne Park, which to the best of my knowledge has no cast changes or significant design element changes).
"What was the name of that cheese that I like?"
"you can't run away forever...but there's nothing wrong with getting a good head start"
"well I hope and I pray, that maybe someday, you'll walk in the room with my heart"