Most of Opeths material I find to be brilliantly arranged. Mike certainly has a knack for putting riffs together in a natural sounding way. This hasn't always been the case though. Pretty much all of the song structures from the first two albums seems very haphazardly thrown together, but MYAH saw great improvement in this department and it seems to have only gotten stronger since.
On the topic of Watershed, a lot of the arrangements seem quite random and all over the place compared to the albums that came before it. At first this seemed awkward and a lot of parts felt like they don't fit but given time they begin to make a lot more sense. For example, at first, even though I loved Hessian Peel, I couldn't help but view it as two seperate songs. It took a long time before I got used to the structure. I think the thing is they are experimenting quite a bit on this album. It has a lot more 'space' than any of their previous albums, if you know what I mean.