If you have the time and energy for planning, I would recommend doing it on your own. Book all the inter city trains in advance and use the public transport for exploring the cities and nearby places. The benefit of doing this is,, you get to spend time at places which you really liked rather than running on itinerary. Eg. Plan for 4 days in Paris and 3 days in Geneva etc. And have a rough plan of places you want to see.
If you don't have that time, work with local agencies rather than SOTC or other big brands. They will prepare a schedule as per your requirement.
You will spend 30-50% more if you go via agencies