CHOOSE OPTION 1
You are in your 30's and are travelling westwards. This means you've got everything going for you and will have no time zone fatigue, quite the opposite. You have put in some sterling work planning this journey, and the layout is so good it has to be assumed that handling words and images is your occupation. Here's some advice:
GENERAL
Travel north to south to make the most of the available daylight, which is decreasing noticeably in the north at that time of year. Arriving in London NOV 15 i better than arriving DEC 15. You will likely be overwhelmed by Christmas decorations everywhere anyway as consumerism is on the increase. Rome was lovely in January as the light doesn't ever change that much down south. I was preparing to recommend Greece, but you have already included two Greek destinations. Don’t desert them. 11 hotels can be counted. Consider always staying at least 3 nights as changing hotels is a hassle and eats up time.
London / Paris
This city is unbounded. 1-2 nights could be added when you’ve come all this way to experience the jewel in the crown of this former, quite short-lived, empire. See a play. Walk Hyde Park in the darkened Victorian evening, autumn leaves falling in the mist, feeling as though you are in Elephant Man (1980) or Dracula (1992). Don’t add nights to Paris unless you are Parisophiles. Malmaison, d’Orsay, Fontainebleau.
Strasbourg / Zermatt / Zürich
Add one night to Strasbourg. Zürich (pop. 400 000) is a good choice for another Swiss city. Chocolate, nice old buildings, trams and a lake.
Florence / Rome
This is the one destination on your list that should be studied scrupulously, with an industrial strength magnifying glass. Read reviews, trip reports and replies in the forum to divine if Florence is a travellers haven or overrun, stampeded and prone to putting you In the Mouth of Madness (1994). Let me go against the grain here and contradict the probable replies of each and every NA or UK responder and suggest that you abstain. The David sculpture is overrated as his mentor, Donatello, is the superior artist. My recommendation otherwise, is to stay 3 nights in lovely walled Lucca and day trip to Florence one day and to Pisa the next day. They are minutes away by train. I would concentrate on the Bargello, see one of the open air Davids and then have gelato.
Rome has more museums than anyone could ever wish for, and you could add 1-2 nights (or a whole year) as Rome is eternal and unending. Be wary of the Vatican/Sistine places, where you are as cattle to be herded through a pen, and read their reviews carefully. Beware the mouth of madness. If you need calm consider a day trip to Ostia Antica or Viterbo.
Athens / Crete
As this is a once in a lifetime trip you must, by all means, experience Greece, which the Roman Empire spent the entirety of its existence trying to emulate. Crete gets the last of the remaining heat. I have swum from its beaches in October. Stay in Chania or Rethymno. The Palace of Knossos is interesting but optional.
Athens is a capital that, in contrast to all other capitals, holds only a fraction of the amount of museums and temples that should be found there. Acropolis, one more temple and 1-3 museums, when you are the jewel in the crown of the entire ancient world, beholden only to Egypt, is hardly even a beginning. Go there, see the sights, and day trip to Epidauros and/or Delphi. Prepare yourself for the ancient languorous ambience of Hellas by watching Picnic at Hanging Rock (1975). Let the sun blind you and the waves speak to you, like they have done since time immemorial.
Prague / Vienna
Three nights in Prague is all you need, as it is circumscribed and not that exciting. I went to a small suburb in the wooded hills for the evening. Choosing Vienna for your last stop is a fortunate and rewarding decision. Wunderbar!