ZRH: Big(ger) airport, more facilities, more orderly.
GVA: Crowded, small airport.

Both can be reached by train easily, but GVA has about 500m walk from the station.

Security: If holding no status, ZRH wins clearly. GVA often has long lines. They've an automatic priority system, which does not work always. Then you're forced to go to the regular queue.

Lounges: I can only compare the Swiss and Air France lounges.

Swiss lounges, I prefer the one's in GVA over the ones in ZRH.
Air France, about the same I would say.

In the end, if both options are equal, I would pick GVA slightly over ZRH if you're holding status, but without status, ZRH is a clear #1.