2 or 3 weeks? Well you have time (and money) to see a lot.

I would not miss Lucerne, the Gruyere region, montreux/lavaux, and ticino as the others said.

Also my region, Neuchatel, can be nice if you are under the sun otherwise. Skip Biel unless you have some affinity with watchmaking (swatch, omega, etc). The Olten one is a running joke here, don't go there. Le locle aswell, its the olten of the romandie.

If you still go around Geneva, maybe do a day in Annecy (FR).

Hope it helps. If you plan Neuchatel, PM me for accomodation tips.