I'm not sure that Aaron Tveit's work in Next to Normal was overlooked for that reason. He didn't get nominated for the Outer Critics Circle or the Drama Desk, although in both cases, he was likely hampered by the fact that Next to Normal's off-Broadway run was in the previous season, and the nomination would have had to have come in that previous year.
You may be right, though. The Tony nominees that year were 4 expected nominees -- Greg Jbara for Billy Elliot (who won); Will Swenson for Hair; Marc Kudisch for 9 to 5; and Christopher Sieber for Shrek -- and one completely unexpected nominee: David Bologna for Billy Elliot. I did not see Bologna myself, but I don't think anyone was expecting him to be nominated.
I believe Bologna did an even split in the role with Frank Dolce, so he only did 4 performances a week. He may be the only Tony nominee to be nominated for a scheduled run of fewer than 6 performances a week.