Don't take your shirt off on the plane. That's just wrong.
If it gets too warm for the provided pj top, I suggest carrying a very lightweight t-shirt with you to change into. Like a Reebok Speedwick.
At home (and in my hotel room) I sleep unclothed by choice. I hate the way clothes get twisted around while I sleep. But on an overnight flight, even if pjs are on offer, I change into that t-shirt and it's matching jogger that I'm carrying in any event as part of my travel wardrobe. They're about as comfortable as anything I've found.