Much of a muchness, imo.

traffic:
NCE is on the western edge of NCE, allowing for a quick exit. That said, the whole coastline up to Cannes is fairly built up and you could get heavy traffic westbound in the evening rush hour.
Lyon is a much bigger city than NCE but the airport is sufficiently far away from town to avoid the more congested area. If you are heading south, you''ll probably take the A43 motorway (which is the Lyon bypass motorway). My recollection is of an easy drive but, to be fair, it has been a while since I have used it.
I would disagree with the previous poster about flying to Paris, unless there is an overwhelming reason fare-wise to do it. The motorways in the Parisian area tend to be substantially more congested than in either Lyon or NCE and it adds 300 miles and a good 4 to 5 hours to your journey (and motorway tolls).

Ease of renting/returning
Both LYS and NCE are fairly compact, easy to navigate airports and easy to rent/return.

If you are going to several locations between LYS and NCE you may wish to consider renting from one and dropping at the other: it is relatively easy to find a rental with no drop-off fee from the majors rental companies.