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The quality and number of cycle path and cycle friendly routes has increased dramatically. I think the Osmap layer in ridewithgps has them all, from local authority to wider networks (eurovelos).
Morvan is full of lakes, vosges are great, jura is amazing to catch a view of the alps before going there, also full of swimming lakes. But one could also cross more north, cycle from basel to zurich to liechtenstein, go up towards st-moritz or andermatt and approach italy from that side, where there is not so much of the heavy duty traffic found in the western passes.
Anyway @samrensho hit me up if you feel like it
Glws-
andermatt and approach italy from that side
If you choose to go through the Swiss Rhone valley and cross to Italy, I would take the Nufenen pass, the descent into Airolo is one of the best I have done ever.
Simplon pass is shitty, lots of traffic including trucks. If you decide to go Furka from the Oberwald side and descend to Realp, be aware as that is the "shitty side" :)
LeMesjeu
I have done this, there is a banging national cycle path that uses an old railway line