Why are you only considering Giudecca and Dorsoduro? What are your requirements?
I was in Venice maybe 10 years for only 36 hours. I didn't like San Marco (but I missed the Doge's Palace) except in the early morning. The idea of a Hard Rock Cafe in the vicinity is kind of scandalous, in bad taste, etc.
But I found that, as I recall, I could walk across the canal (Grand Canal??) to the Dorsoduro side. There I found, during the day, the beauty and quiet I had been looking for, in the vicinity of the Accademia. I was speechless in front of the Salute. I vowed to come back and not spend a hurried 36 hours on a group tour.
(I have a graduate degree in art history and am particularly interested in Tintoretto, Titian, Bellini, Palladio...).
I am under the impression that Canneregio or even Castello might be more of the "real" Venice. Dorsoduro has a lively night life near the Campo Santa Marguerita (sp?). I want to be far away from that. But Giudecca seems not to have the same charm as what lies on the other side of the Giudecca Canal in Dorsoduro "proper." From the Youtube videos, it seems almost like a "warehouse" district." But not as working class as San Polo (or is it Santa Croce?).
Anywhere away from tourists and a high concentration of hotels that cater to them would be acceptable.
I'm from Seattle, where the public transportation is quite abomindable, where buses are frequently 30+ minutes late or simply don't appear, which is why I balk at not being able to walk to where I want (even in Rome, sometimes I waited 40 minutes for a bus, which never appeared) and to be at the mercy of public transportation (Paris is good, in this regard).
I did take the vaporetto once or twice. Maybe it's just a question of getting used to having to queue and stand on a small motorized boat for a few minutes.