If all you are doing is using the car to drive between cities then I would seriously consider taking the train option. The autoroute between Geneva and Zurich goes straight up the plateau and is not very scenic. It can also be very congested as it is a main route south for many Germans, Dutch and Belgian tourists, though September would be less congested than August. I drive that route frequently but also take the train out of preference if I don't need the luggage space. The train service between Swiss cities is excellent and very frequent on clean, comfortable carriages. If you want to go to the italian speaking part, Ticino, then train is by far the less stressful way from Zurich to Lugano. Trains also give you the best of what scenery is on offer and more often than not timetables are integrated with the smaller regional companies which can take you into the mountains etc. You could buy a half price railcard which is excellent value. I've never used Elite so can't comment but then again I only had good experiences with Europcar. Remember most Swiss cities are small and you can easily get round the historic centres on foot so even taxis are not necessary.
Let me join those suggesting travel by rail. For an excellent analysis of the discount offers for tourists see ChrsW's excellent post Travel Passes for Visitors .
I would also go the train route, the system in Switzerland is excellent and you will see a lot more of the country from a train than you will from driving on the highways.
I agree with the other posters. With an extensive rail network, this is the best way to travel. They are as scenic, if not more so, than driving, and certainly more relaxing. I have had no problems with luggage. There has always been plenty of space. I haven't travelled on the main commuter routes in rush hour so I cannot say what they are like. I understand that they can be quite busy.
You can have your luggage sent on separately if you prefer:
Plus, in general, driving in switzerland takes way more than going by train. Let alone finding a parking place, the cost of the parking, the very likely possibility of fines if you are not familiar with the traffic laws... ecc ecc ecc...
Just looked out of curiosity: Google Maps and SBB timetable show identical times for driving and train from Zurich to Geneva, 2hrs 43mins.
The train will take that long and you can have a meal and drink on board. Driving could take longer with fuel stop, break, traffic delays etc. plus all the other problems mentioned.
I agree with the others that the train is the way to go, luggage wont be a problem if you can carry it, there is always enough space.
For the car - the rental agency you mention looks super expensive (2-3x the price with limited km). I always use Europcar and have never had a problem, not sure what you have heard...But maybe I am just cheap and can't imagine paying for anything with the word elite in the name!
Thanks for the input all. I agree with you all and will b taking the train as that ways I wont have to worry about getting fined or getting the car wrecked.
Maybe on my next visit I might consider renting an elite car(Lol)
But thanks again everyone.You all were very helpful