a) by train: it’s comfortable and on time.

But:

you are tied to a schedule, burdened with your luggage, may have to change trains, what if you miss a train?; and pay for taxis once you get there.

b) By rental car: great idea, flexible and independent,

but what is the reality? Car traffic in Europe is aggressive and often chaotic; by the time you’ve learned to read the directional signs your are already lost a dozen times; searching for an inner-city hotel address and parking may be nerve-wrecking; the unfamiliar driving experience is dangerous and exhausting and takes the fun out of sightseeing.

c) by 50-seater coach: it can be comfortable, alright,

But:

you are right in there with the programmed mass-tourism you wanted to avoid. Where’s your individuality? Instead you have fixed schedules and a big crowd.