Why not stay in both? They're close to each other. I'd recommend 2 nights in Ghent and one in Bruges, but I'm biased in favor of Ghent.
In order to avoid having to pack up and change hotels, 3 nights in Gent make more sense. Brugge can easily be done as a day trip.
I agree, the less switching hotels the better.
As you put this question in the Brussels forum, I assume you're also visiting Brussels, in which case Ghent is roughly halfway between Brugge and Brussels, so you could (slightly) more easily visit both from there.
On the other hand, some people prefer to be in Brugge after the day-trippers have gone, and travel time from Brugge is not that much more - plus, you don't keep having to get a tram to the station as in Ghent, assuming that you would want to stay in the centre.
The way we have it now, we will be going to Ghent from Amsterdam. We will stay 2 nites. Then go to Brussels and stay 2 nites before heading back to the US The only reason why we will go to Brussels is because our plane is in the morning and we want to be near to the airport. Also, we were never in Brussels, so visiting the capitol is important. Sort of like going to Greece without visiting Athens.
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