Apart from the price, the departing airport could be a reason. But I do not know what type of traveller you are. Personally if I were the "early at the airport" type of person I'd prefer AMS; for getting through quickly, GVA.
If flying Star Alliance, GVA; for Sky Team... (you get the picture).

And are you looking forward to snow in Annecy/Genève, or wanting to avoid it? (In case your trip takes a few weeks...)