Having done both I would take a car at Geneva from the Swiss side if the price is close enough.

Might be coincidence but I've generally had better kept cars picking up from the Swiss side. Also very important if picking up between, say, November and March : French side will not give you winter tyres unless you pre-order and pay that special option. Swiss registered cars will have winter tyres already on them. It does make a difference if you drive out onto a snowy motorway and realise the winter tyres you took for granted, are not on the car. I've done it one scary night when I had a long journey, and would not recommend it.

At Hertz Geneva late one night I was also given a form with extra insurances that I had previously declined, and told the desk I did not want, when I picked up. Assuming when I told her I did not want these extra insurances this would be respected, and as the desk lady had stayed open for longer as my flight was late so I felt sorry for her, I signed the form she printed out without checking the back page overleaf. Extra insurances turned out later to be "ticked" on the reverse side of the form. Mistake. On mentioning these unwanted insurances when I returned the car I was told that as I had signed, nothing I had specifically said mattered. So a reminder: even in a "respectable" location like Geneva, I suggest you check the form you are asked to sign does not include things you refused.