If I just wanted to get from GVA to ZYR, I would strongly consider going by train all the way. I haven't checked prices, but you can do it by TGV in 6hrs, with just one change in Lyon. Personally, for this sort of distance/time I find a journey by train much more productive (as I can board the train, and immediately find my seat and start to read, work, etc) than flying (having to reach the airport in time for check-in, go through security, wait to board, shut-down electronics during take-off and landing, wait for baggage, etc).

However, if (as I suspect) Cupart wants to maximise FB miles and segments, then you may also want to look at Alitalia. At least in theory, they have some reasonably attractively priced fares for GVA-BRU, all of which would earn miles and 4 segments. However, flying via FCO is not the most time-effective option; you have to build up the routing using the multi-city tool (otherwise it just shows the KLM options); and you must avoid the code-shares operated by F7 (as they don't earn FB miles at all, being non-ST).

And of course, as Henry III mentioned, AF offer GVA-CDG-ZYR as well - with CDG-ZYR operated by Thalys (2H) and coded as AF, so it seems these earn miles and segments.

Assuming reasonable availability, I suspect the best balance of cost/time/FB miles lies with AF...