I bought an AT, not because I really wanted one, but because the van I found  was otherwise perfect.  I was looking for a clean Westy with a near-dead engine (I knew I wanted to install a Subaru engine).   My concern about an AT was that it robbed power from an already under-powered vehicle.   However, my research revealed that the AT in the vanagon is probably a stronger and  superior transmission to the manual.    
    I have to say that the van I bought drove like a motor boat with a trolling motor.  I have no experience with driving manual vanagons, so I have no point of comparison.  I don't know whether my van was so slow because of the AT, or because the engine was dead, or both.  But it didn't cause me problems for long.  Shortly after buying the van I dropped it off for an engine transplant.  I picked it up 6 weeks later with new life.  My pre-purchase and pre-transplant concerns are no longer valid.  The van now drives like a real car.  I can drive uphill on the freeway, and pass other cars (many of who have been shocked).  It can actually go 90 on Hwy 5 like all of the other speed demons.  
    All of that aside, I have found that I really appreciate the AT for everyday driving.  As a starting point, the vanagon is not a performance car, no matter what kind of engine it has.  The manual trans has no significant advantage over an AT unless one is seeking high performance.  My daily driver (was) (is) a Porsche.  I didn't think I would ever admit that I would prefer driving an AT to a manual, but I have to admit that do.