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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
Going through france, there are loads to see -obviously - I'd recommend thinking in terms of areas to cross, what vibe, level of remoteness, etc. you seek. My opinion but a straight path from paris to dijon isnt the most endearing.
Maybe the Vosges then some black forest, constanz lake ? or head to Jura via Morvan ? There are wasy to cross to switzerland in a different way than Lac Leman.
Or If you like architecture maybe plan around staying at La Tourette convent near Lyon ? Just random ideas.
It's also important to pick nice passes to cross the alps, car traffic varies dramatically