Not really the train fare is huge from Zurich to Geneva so sort of brings an abrupt end to the idea of a "cheap" flight. I'm sure there's ways to bring it down though.
Then again a convience thing +3 hrs on the train to geneva is a PITA
I think its all about demand. If the demand is high then the cost reflects this demand. You would like to think that high demand means a better price but the world no longer works like that. Just another way to make money faster.
I must admit I have only used geneva twice, and while zurich is spacious, clean, organised, and well Swiss, Geneva is small, cramped, dirty and, well, french
Normal enough. In many places such as the US, fligts are more expensive out of major hubs than through them. Demand is part of it, though I often heard - unconfirmed - that government subsidizes routes to less popular stops to maintain availability.
If you are time-rich and price sensitive you are often advised to HUB-SWAP. This is the practice of taking a short-haul flight from your local hub to another - and then the long-haul flight.
The hubs are where major carriers are based - and so try to tempt rival airline passengers with lower prices. If you are flying from LONDON it is often cheaper to hub-swap to Paris (Air France), Frankfurt/Munich (Lufthansa), Amserdam (KLM), Zuirch (Swiss) than it is to fly BA from Heathrow.