Mid/End-September is around the very early beginnings of Autumn, it depends on the part of Europe; but Germany/Prague will be in the 15-20 C range, which is nice and cool (it's the Genting/aircond temperature range). Summer is generally from Mid/end-May until August; with slight fluctuations now that the weather here has gone completely bonkers! It's snowing here this week and it's supposed to be Spring!
I like Sept-late Oct/Early Nov. It generally goes in the 10-20 C range, which is perfect for my wife to wear shorts and slippers still.
Depends where you go. Also; the further east you head, be careful! The temperature peaks during the day and can go to 20-25 and the drops at night can be quite sudden; and drop as low as 15 or so. I fell sick once in Poland in June because it was 30 C and freaking hot during the daytime but suddenly dropped to 15 C with bad winds at night. I was still out (after dinner) with shorts and short sleeved shirt without layers because I thought I would be over-dressed!
The locals could be used to it; but be careful!
Also; Oktoberfest tends to be over-rated; most locals tend not to go to Munich during that time period but celebrate it in their local pubs/beer gardens. Apparently; each City has a special way of spending Oktoberfest. When we were visiting Austria during the Oktoberfest; there was a music festival every night in the city we were staying at (Graz).
The temperatures around the mediterranean coast are the warmest in Europe. It's still quite comfortable during winter! I've noticed that France tends to be warmer than Germany/Prague in most cases. The weird thing was Vienna (during my trips) had been colder than Prague; but I was told it's due to the landscape causing the temperature differences; so that plays a part too. Apparently...
Having used the EUrail pass previously; my personal opinion is that from Prague onwards east, train ticket prices are very similar to what you pay for in Asia; so I wouldn't get the EUrail pass if you're headed that way (After Prague). Use the EUrail pass in countries which are $$$, Central Europe generally. Otherwise, some budget airlines could be really cheap; but train could save you an overnight hotel (and time!) Also; remember that EUrail passes don't cover the cost of reserving a bunk/bed.
Looking at your country list, it's not bad, but I have personally been told Bratislava's quite boring and not more than 2 days/1 night. But why Zurich? That's the most boring (and $$$) place (in my opinion) out of the whole of Switzerland...
My sister did a 5-weeks EU trip last year, and she did the below:
Netherlands (Amsterdam, a couple more small towns)
Belgium (Brussels, Bruges, Antwerp, a couple more small towns)
Luxembourg
Germany (Frankfurt, Munich a couple more small towns)
That took her about 16 days or so; I guess they didn't rush it though. Then she met me (I drove from Prague) on the outskirts of Munich and we went to the below, took about 15 days:
Germany (Fussen to see the famous "disney" castle)
Switzerland (Zurich, Lucerne, Interlaken and surrounding towns/hills/villages, Zermatt, St. Moritz)
Austria (Salzburg, Hallstatt, Vienna, Dachau)
Czech Republic (Cesky Raj, Bohemian Switzerland, Bastei (in Germany), Prague, Cesky Krumlov and some other towns)
Then they left and covered Berlin and couple more towns before flying out of Amsterdam.
The general rule in Europe is #1: There's no such thing as FREE THINGS!!! So; if people approach you to give/do things for you; remember #1!!
I personally like Autumn; less people and the weather is not as weird/fluctuating as Spring. Spring weather can sometimes feel like Winter; depending on where you are. Just last weekend; Prague weather was really weird, raining and cold wind in 1 part of the city while sun shining in the other part. Really bad winds though. And this week is now snowing! Although today's sunny now though...
Luxembourg boring for me..