Yeah, I really wouldn't stay at Mestre if possible - you miss the best part of Venice (mornings and evenings, when you can stroll without worrying about catching a bus or train back to Mestre). It may sound like, "Oh, I can always take the train whenever I want to," but it just doesn't work out that way in my experience. If you have to worry about what time the last train is (or waiting 30 min for one or something), that kind of ruins the fun. Or in the morning, you can't just roll out of bed and go for a walk.
But if I HAD to stay in Mestre, I'd surely stay right at the train station - there are hotels across the street (not sure if they are nice or cheap). From there, at least, I could hop right on the train to Venice, and I could catch an airport bus in the morning from there. Then again, if you say near Piazzale Roma on Venice, you can achieve basically the same thing (catch an early airport bus in the morning).