Your route involves a traverse of Geneva - two things can happen here, you'll get lost following the very poor signage, or you end up directed onto the autoroute blanche to Annecy and paying a 12 month Swiss motorway vignette for half an hours ride. In any event the traffic will add half an hour to the plotted journey time and worst of all, you'll be in Geneva! I would definatly stay on the French side. The run down Lac leman (Geneva) looks nice on a map, but is very dull in practice. this part of the world is very densly populated, in the summer, you'll be in traffic the whole time.
So here is a nice route, most of which I know well.
Steinsoultz is in the Sundgau, a part of Alsace known as the Mille Etangs for its profusion of lakes (and excellent freshwater fish cuisine). The route crosses a 'sticky out' bit of Swizterland and heads to St Hippolyte on a great open twisty bit of road with plenty of 3-lane overtaking sections. Watch out for les flics, the road has a bad reputation for moto hooligans. St Hippolyte should take around an hour so a cafe creme and a croissant (from the boulengerie across the road) might be appropriate at the biker cafe - you'll know which one it is.
The big wide twisties continue until Maiche (again watch out for police) and then, continuing to climb into the Jura, to a giddy descent to Biaufond on the Doubs. An old customs station, beautiful lake and tales of smugglers abound. The gorge of the Doubs is spectacular here. If you happen to be here at lunch there is a fine Franco-Japanese (no kidding - think carp sashimi) restaurant on the swiss side next to the lake.
Now an amusing twisty ascent up the Swiss side of the gorge to the very dull Chaux-de-Fonds followed by an equally dull (but thankfully short) passage through manicured swiss countryside until the descent to the Doubs and Villers-le-Lac, Morteau (speciality sauasage) and then a beautiful run along the Doubs to Pontarlier in the heart of the High Jura.
Passing by a couple of lakes on the way, then a classic High Jura run along open curvy roads, loads of overtaking possibilities (in the rare event you come across traffic) and kilometer plus visibility to St Claude. Then a really nice run up the side of a chalk cliff out of St Claud eventually to Bellegarde-sur-Valserine.
Between there and Annecy, my recollection is more hazy, but there be mountains and there be twisties.
This route is 331 km, 5hrs, the quickest possible route is 291km 4.5hrs for which you'll need a Swiss vignette or to get lost in Geneva, probably both. Its 30km and 15 min longer than your route through Nyon. My route will put a smile on your face, I promise.