I like how way back at the beginning of this thread you see a couple of the standard forum response: That comes up all the time, do a search. Then when someone does a search and consequently resurrects a dead thread, they get called out for that. You really can't please everyone.
But I like this thread because it's got a lot of info and a lot of people chiming in with a lot of experiences, and it's all in one, handy package. Some thoughts on the subject at hand:
Ease of travel: I would agree that trailers are trickier than panniers on the plane/train/bus. Probably. I am planning a trip where I'll be, hopefully, doing a Bike-Friday-style move where my luggage becomes my trailer. The whole point of this set up was to make travel easier and cheaper. I hope it works. If so, one point in favor of the trailer.
Weight differences: I can see where there'd be a temptation to overload a trailer. Or rather to take more gear than you need, just because you can. I'm guilty of that pretty much every day, touring or not. But if you control yourself, it seems like trailer still has potential to weigh significantly more. I've been trying to get my gear down to two (admittedly large) panniers. If I can pare my gear down enough, I could potentially lose the weight of one rack and two bags. So not only would my actual gear weight go down, but the weight associated with the base carrying system would go down, too. A similar reduction in a trailer gear results in no less weight of the actual trailer. If I can get my gear down to two panniers, that's one point in favor of the pannier system.
Also, for my upcoming trip, I want to take a folding bike because it's easier/cheaper to transport. A downside is that it's hard to arrange my rear panniers so that I'm not kicking them. If my heal strikes my trailer, I know I've done something very wrong.