What does "seeing a city" mean to you? In your plan you get two full days in each; if all you want is a quick glimpse of a few major highlights, it's perfectly doable. However, you might well end up feeling you've just seen a succession of postcards; you really won't have time to get a feel for any of them, especially given that each is in a different country with very different languages/culture. And don't underestimate how tiring it is to to re-adapt to a new country each time, in your program, you barely have time to work out how to get a bus ticket before it'll be time to move on to a different system.
Also, out of 17 full days in Europe, you have five given over to travelling- that's nearly a third of your time in transit. Fine if you enjoy the travelling part - for me taking trains or buses through the country and seeing the landscape is part of the fun - but your post sounds as if you just want to get that part over to reach the next place. You won't get much else done on travelling days; flying is theoretically quicker, but as has been said upthread you won't save much time once you've factored in getting to the airport, check-in time and so on... Trains will get you town center to town center, so you need to check out just how long you really need to get to and from each airport and the price, and how early you have to be at check-in, before you can really compare which is the most efficient. Personally I would fly to Rome and Barcelona, maybe Munich out of your list. London and Amsterdam are both about 3 hours from Paris by train, so faster than flying, also easier to get convenient departure times.
The rest is personal taste, what do you really want to see in each place? Famous monuments, architecture, history, art, food? You could spend a month in some of your destinations without getting bored, depending on your interests.
I would just advise you not to get caught up in the "I've come all this way so I must see everything" syndrome: you won't see everything whatever you do. There are literaly hundreds of worthwhile places that you won't see just in the countries on your list. In leaving one place you give up on the other things you could have found there, if you stay you pass on somewhere else - you'll see the canals in Amsterdam, but not the catacombs in Paris, or vica-versa, so there's no point in stressing over missing out on something. Just make sure that you travel the way you enjoy travelling!