… there may be a big disadvantage to sleeping in a shelter versus choosing a tent. Hantavirus! This nasty affliction is spread by rodents, especially mice. Mice habituate shelters, and hikers tolerate them. …
Privacy – You aren’t a stuffed sardine when it gets crowded.
Warmth – A tent with a rainfly is warmer than an open shelter.
Better Sleep – You are not poked, or kicked, or outsnored.
No Mice – Those critters can drive you nuts!
besthike.com 
I shared a shelter in Baxter State Park, ME with my brother-in-law and it was the best night sleep I ever had camping. It was clean and spacious. The following night I rented a cabin and wandered to my car in the middle of the night to get some sleep. No air.