We spent a little over a month in Switzerland with a car a few years ago. Besides the expensive petrol (!!!) there really isn't a downside IMHO. There are MANY places that a car can take you where trains can't go...there are also places trains can take you to that cars can't. Zermatt would be an example of that...but you park at Visp, spend however much time in Zermatt you want to, then get your car and move on to the next destination! There are some train routes that traverse spectacular passes that you can't see from your car but the opposite is also true. Since you'll have two weeks or so, the flexibility of a car, without being tied to train schedules, makes for a leisurely trip. I do prefer not having to drag suitcases to and from train stations and on and off of trains. I LOVE to drive and some of the roads in Switzerland are a lot of fun if you enjoy hairpin roads and views! The roads are in excellent condition. If you get into some of the more remote mountain passes (which I highly recommend) there are some that are dirt but they're maintained and relatively smooth.
Parking is not an issue at all in Switzerland. If you rent the car in Switzerland it will come with a vignette for driving on the motorways - otherwise you will need to buy one at the border. Know that speeding laws are strictly enforced by cameras. Tickets come automatically in the mail. By the time it would get to you it will be quite expensive so be very aware of the speed limits. It is no problem to take the car into Germany but, it you return it there, there will be significant fees for doing so. It will be far less expensive to return it in Switzerland, or whichever country you pick it up from.
