Just stayed at the Molino Stucky Hilton (Venice)
It is true that the Stucky is on Giudecca, across the channel from the main islands, but there is a free (scheduled) shuttle boat to two stops: Zattere directly across the channel, and another stop adjacent to Piazzeta San Marco. Thus, it is not nearly as big a disadvantage as you might think. You can also take the vaporetto to 2 nearby stops.
This Hilton is very nice. Quite a large and striking building, and lovely to look at the city across the water. I would stay here again, no doubt. Arriving at the trains station it is easy to get to on the vaporetto- five stops I believe. Easier than many other hotels in Venice.
If you go in the flooding season, though, you should take care to wear rubber boots or get back before the those stops become flooded. Boots are readily available for purchase there for less than $20 and are commonly worn on days when overtopping of the lower elevations is likely- depths are typically from 1-3 inches that I saw, except for Piazza San Marco, which might have been a bit deeper. They set up elevated walkways that cover most, but not all major routes.