Please help refine my itinerary

Any possibility of reversing the direction? Starting in Athens and ending in London. The Mediterranean section will be hot, and early June there will be a little cooler, then working northward into July.

I think they call this the Salesman's Dilemma Mathematics Problem. How to connect a route with all the required sales calls in the most efficient manner.

One little thing, Colmar is only 30 minutes by frequent train from Strasbourg, so it can be easily done as a day trip from Strasbourg, or as a stopover between Strasbourg and Lauterbrunnen. So that is one less overnight to worry about.

Thank you, Sam.

I got tickets few days ago. Chose London as I read how starting the trip from English speaking country is easier.

Starting in Athens actually sounds perfect weatherwise. I prefer cold weather than hot. I will check the cost of changing the tickets and if the difference is relatively okay will reverse the direction.

Will look into Colmar and if it looks do able then save 1 night there.

Skip Amsterdam and take the Eurostar to Paris. Buy your Eurostar tickets now because the further out you buy train tickets the cheaper they are.
I agree with Sam, sleep in Strasbourg and take a day trip to Colmar.
Have you considered visiting the Bavarian Alps instead of the Lauterbrunnen Valley? Logistically it will be much easier than spending a couple days trying to reach a destination in the Berner Oberland or Zermatt. You can then fly nonstop from Munich to Venice. Add a night in Venice.

Some of your proposed visits are difficult to geographically reconcile with your overall plan without serious backtracking.

For example, starting in London planning Amsterdam then Paris. I suggest skipping Amsterdam for this trip.
Also, Barcelona is just way out of the way, skip it and plan to do Spain later.
Further you include Munich, Berlin and Prague, then plan to see Switzerland then Italy. Not sure how you manage this without backtracking. You might consider skipping Germany and Prague this time.
For Italy, plan more time in Rome, four nights is not enough. Cinque Terre is nice, but consider skipping for this trip.

I have been to all the places you list and have my own preferences, doesn't mean that I am right, but Barcelona is a great place to visit, but Italy will wow you more. The Amalfi Coast is similar to Cinque Terre, but more awesome. Florence deserves 4 full days.

I suggest that you plan your transport and lodging every step of the way for your trip. TripAdvisor.com is a great resource for lodging and has a great map feature that helps picking hotels at the best location.
It is important to know just how long it will take to go from place to place, so you can factor that into your itinerary.
Example, train from London to Paris, X number or hours.

I will take a shot at this.
1. London to Paris on the Eurostar. Takes 2 1/2 hours. Hourly departures.
2. Paris to Berlin by airplane. There is a direct train, but leaves at 10 am and arrives at 6 pm, 8 hours and killing a whole day. There is also a night train, but that is every other day and takes over 13 hours from 7 pm to 8:30 am the next day.
3. Berlin to Prague by EC train taking 4 1/4 hours. A train every 2 hours
4. Prague to Munich by direct train taking 5 3/4 hours. A train every 2 hours
5. Munich to Strasbourg by train. One direct train in the morning. Takes 3 3/4 hours. Other trains with connections
6. Strasbourg to Lauterbrunnen. Takes 4 hours with at least 2 connections. Frequent trains.
7. Lauterbrunnen to Zermatt. Takes 2 3/4 hours with several connections. Frequent trains.
8. Zermatt to Venice. Takes at least 7 hours and at least 2 connections. Italian rail schedules are still not firmed up for after June 14. Possible a stop in Milan about half way.
9. Venice to Florence. Takes 2 1/4 hours by frequent direct trains.
10. Florence to Rome. Takes 1 1/2 hours by frequent direct trains.
11. Rome to Barcelona by airplane. Takes 2 hours flight time with several direct flights through the day.
12 Barcelona to Athens by airplane. Takes 3 hours flight time with a handful of direct flights each day.

This seems to be a 6-1/2 week trip. You have laid out an aggressive schedule with rather short stays (though not crazy-short) in many major cities with dozens of sights potentially of interest. I think you'll struggle to keep up the pace over such a long trip. Personally, I hate taking even one flight in the middle of a trip, so this itinerary is not something I'd even contemplate, but you may be a lot more tolerant of the getting-to-the-airport issues than I am. Be sure you consider the time lost for each of your major moves.

Barcelona and Berlin are two of my favorite cities. In the context of this trip, on which you have so much ground you want to cover, I wouldn't go to either of them for just 3 nights. Just two full days and perhaps some hours in either of those cities would be very frustrating to me. As already mentioned, you can see Barcelona as part of a trip to Spain (or even southern France), so I think it's a candidate for elimination this time around.

Two nights is short for Venice.

I wouldn't go to Greece just to see Athens. The city has, obviously, some very important ancient sites and related museums, but it isn't otherwise a particularly attractive place. There are many interesting destinations in mainland Greece, plus the wonderful islands. I'd hold off on Athens until I had time for a more comprehensive visit to the country. I realize you have an airline ticket that has you flying home from Athens, but I'd really rethink that.

Being that the OP has a 26 hour flight to get London (assuming coming from Auckland), I can see trying to cover as much ground as possible. It is easy for us with 7 to 9 hour flights to say "do it on another trip".

@ Sam : That's right. Will be coming from Wellington :). By the time I save enough leave, I miss home and go visit mom which is 30 hours to other side of the world.
This trip will be basic one to cover more cities now to find out which ones I like more. So hopefully, whenever I visit home in future I could stopover a week or two to Europe and focus on one or two cities at at time. I do have Japan and Vietnam for next year so not sure when I will back in Europe.
Thank you so much for the itinerary especially with the transportation suggestions as well. I really appreciate it. I might remove either Berlin, Barcelona or Prague to add extra day in other big cities. I will move the cities in that order.
Couldn't reverse the direction as suggested as it would be extra $800.

@Matt : Yeah, I will remove the Amsterdam. I didn't know about the Bavarian Alps. Might add extra day in Munich and go there. Also, will look into only one base in Switzerland and go to other places for hikes.

@Geovagriffith : I will start looking into tripadvisor for ideas. I might remove eitthr Berlin, Prague and Barcelona at this point.

@acraven : I actually like airports. So much that I have missed flights because I was too busy looking around and missed my name being called. But you are right, I don't really know how long/difficult it will take me to reach the airports from the cities there. I'm a bit worried about that. I looked for best islands and beaches and some islands near Athens came up. That's how I got the flights back from there. I have to be there for return flight but maybe I will check if I can fly into nearby beautiful island from Barceolna instead and just stay there until last day to Athens.

Thank you so much all. I really really appreciate your input :)