Having done ZRH-GVA many, many more times than I care to count in both directions, may I recommend the plane.
The flight itself is REALLY quick and very scenic, even (especially?) at night with the moonlit snowy mountains [1], which are to your side, not under you (try to look south), and the stars. You're barely getting used to being in flight and they are already handing over the little chocolate and asking you to fasten your seat belt. Both ZRH and GVA (especially GVA) are ultra fast airports where check-in and security are a breeze (I recommend the mobile boarding pass) and there is fairly little walking. You can definitely door-to-door it in much less on the plane even with checked-in luggage (unless it's substantially changed in the last 3-4 years). Price wise I used to fly that route for 30-40 CHF, very competitive. It was sometimes cheaper to fly to London via ZRH than direct from GVA.
Meanwhile, whilst there are a few direct trains, most have a stop in the middle to change trains (from memory: Bern? maybe Biel or something that starts with L) and you have to carry your bags back out and stand in the cold for a few minutes and stress about whether you're on the right platform. Also, the bag space in second class is quite limited. On the plus side, you avoid taking trains to/from the airports, or getting frustrated with Switzerland's low speed limits on the highway.
I'm surprised the OP uses North American cities as examples of airport connectors. Hong Kong, Tokyo (NRT) and Shanghai to cite three big international destinations have great airport connectors which make sense considering the distances at play. I've always wondered why planners don't send their team to visit the top 10-20 airports in the world to check what the competition is doing.
Singapore is an example of the airport being close enough that you might as well take a taxi and a rapid transit to the "centre" (what is the centre, anyway - CBD, Orchard? there are a lot of hubs) makes less sense. Montreal's situation looks more like Singapore's than Tokyo's.
London is an example of where the extremely expensive airport connector (Heathrow Express) ends up somewhere with nothing except cheap hotels and slow connections, which is why they're finally getting round to building Crossrail, which goes from the Heathrow terminals all the way to all the major hubs (including the City and Canary Wharf, great news for those who have to fly transatlantic).
[1] https://www.youtube.com/watch?v=_hvWN3jOvvM&t=1m20s