Haven't ever given thought to PJ's on flights actually, hubby tends to wear trackies and tshirt, son wears tshirt and comfy shorts, and I wear tshirt with leggings (leggings are pretty much like pj's anyway), then we change prior to breaky & landing. Nice and comfy, and fresh clothes for the new day also.
We have only just started to fly international flights (prem econ only so far), and we have just started to fly business for domestic flights (we're spoilt now and only want to fly that way for the longhaul domestic flights!) - I am looking forward to the day we get our first set of airline pj's - you should have seen how excited we were with our first vanity bag on the international flight, and then our virgin vanity bag on our first business flight - all those nice little perks.
Back to the pj's - fly in what you want to, everyone wants to be comfy for those long flights.