Wow, I'm really surprised by the results of this poll. Last time I checked, this forum was pretty keen on GR. Maybe not I guess.
But anyway, I've given Watershed a lot of listens... and I would have to say it's not one of their best. Just overall as an album... I used to think GR was kind of weak, but with time I have realized how mature, well-crafted, and occasionally downright beautiful it is. Objectively, I would say that none of Opeth's albums are really 100% no-questions-asked masterpieces, but then most bands are unable to achieve that feat as well. Each album has its weak track or tracks in some cases.
But just in terms of GR vs. Watershed... Watershed honestly has no song even close to the awe-inspiring splendor of Ghost of Perdition, Baying of the Hounds, or, to a lesser extent, Isolation Years. It just doesn't. There aren't really any "bad" songs, there just aren't any particularly great ones in the vein of GoP, BotH, Blackwater Park, Deliverance, The Moor, DotF, and all the rest of the Opeth classics. I would have to say Heir Apparant is the best song on the album, because it comes closest to achieving that glory, but that is unfortunate because it doesn't come that close.