Four countries is an awful lot to see in three weeks! I'd try to prune it to about half as many places and go back to the other half on another trip. My spouse (who is hyperactive and runs around at high speed from dawn 'til dusk when on vacation, and once used a three-day break from a conference in Switzerland to visit both Grindalwald and Svalbard, the latter of which is well above the arctic circle...) has, however, come up with the following schedule for how to fit in almost everything you should see if you really want to do it all:
Day
1 Fly to Frankfurt
2 Fly to Frankfurt, rail to Paris. Photo Notre Dame at sunset, Defense Arch at night
3 Photo Paris
4 Rail to Versailles, RT, photo
5 Rail to Chartre, RT
6 Rail to Geneve / Interlaken / Wengen Switzerland. Photo alps sunset
7 Photo Grindlewald area (Lauterbrunen)
8 Photo Grindlewald area (First)
9 Grindelwald area Jungfraujoch. Return to Wengen on Wengenbahn loop
10 Rail to Zermatt
11 Photo Zermatt - Gornergrat railway
12 Photo Zermatt, Matterhorn Hutte.
13 Rail to Venice
14 Photo Venice
15 Rail to Rome / photo Rome
16 Photo Rome
17 Photo Rome / St.Peters (Walk).
18 Fly to Athens, Photo Athens
19 Photo Athens
20 Overnight tour to Delphi
21 Return from Delphi, Fly to Frankfurt
22 Fly home
Still, I personally can't recommend doing all this that fast. His schedule has only about a day in some places that really deserve four or five. And you'd better like trains, because you'll be spending an awful lot of time on them!
(His recommendation to fly into Frankfurt and take the train to Paris is based on the fact that De Gaulle airport near Paris is an awful airport to fly into or out of; chaotic with frequent delays and difficulties of various sorts. It will be quicker, though probably more aggravating, to fly directly into Paris rather than Frankfurt.)
Regarding how to get around: In France, Switzerland and Italy, trains are the way to go. Don't even think of driving in most big cities in Europe unless you have nerves of steel and a talent for finding parking in the most overcrowded of places. Trains go most anywhere you'll want to go in those countries, and are mostly quite pleasant with nice scenery going by. In Switzerland, a network of trains, funiculars, lifts, and cable cars goes
everywhere the tourist might possibly be interested in going, and are very nice and
oh so scenic!
I'm not sure about the transport situation in Greece. I've been there, but only in Athens or on short tours. I'd recommend taking trains to everywhere else, but then flying to Athens (maybe from Rome). In Greece, the three places most worth seeing are Athens, Delphi, and some of the Greek isles (Mykonos/Delos, or Santorini).
I guess if I were planning a trip for someone else who hasn't been there, I'd focus on Switzerland & Italy for the first trip, and do France and Greece on later trips. Rome, Venice & Switzerland are among my favorite places to visit, and train connections between them all work very well. You could fly into Rome and do the rest by train, or into Frankfurt or some other city in the region if flights (and airline pricing) work better elsewhere. It also helps to do both countries, so you get some variety in the trip, with historic cities in Italy and stunning outdoors scenery in Switzerland. If you're only going to do one part of Switzerland, then doing the Jungfrau region is best, staying in either Wengen or Murren (near-carless mountain villages in stunning scenery with good transport to them). If you have time for a second, go to Zermatt to see the Matterhorn.
You can check train schedules, times and often prices at the following European rail web sites:
www.bahn.de (German rail site)
www.sbb.ch (Swiss rail)
They cover trains not only in their own countries, but in nearby countries too. There may be a similar site for the Italian train company, but I don't know it offhand.
Sorry, I don't know about fall colors.
Lisa