The highlight of the drive between Geneva and Lyon would be the section of A40 after Bellegarde, a Alpine highway spectacular in both scenery and engineering.
Bourg-en-Bresse, a short detour on your way, is nondescript but famous for its poultry

.
The medieval town of Pérouges, just before Lyon, is well preserved and may be worth a stop.
Download this
Lyon guided tours brochure for an overview of the sights. I am personally fond of walking along the Saone river banks, the view from the Fourvière and the quaint Croix-Rousse district.
Some of the outer suburbs of Lyon are quite rough (your Swiss rental car might be victimized). I would park the car for the day and explore the city by foot, as its size is rather manageable.