Suggestions on my Europe itinerary

Every travel day deprives you of most of a day sight seeing. You are traveling 8 of your 16 days so you will literally spend half your time on trains or planes. It's tempting to want to see everything, but you need either fewer destinations or more time. You have 10 destinations. Choose your top 4 and you'll see more and be happier.

This itinerary worries me too. Assuming you're arriving in Amsterdam, two nights mean one evening (with jetlag) and one full day to enjoy the city. One night Bruges, means one short afternoon and one evening. The morning is spent on travelling from Amsterdam (which will take some six hours, including checking out and in at hotels, getting to and from station); and the next morning already finds you on the train to Paris. Those two nights for Paris also means one short afternoon and one full day, which gives you time to see the Eiffel Tower, have a look at the Notre Dame and a short visit to the Louvre.
Much travelling, much stress and little enjoyment. I find it all a waste of your time and money.

Lake Como ( i guess i have to keep base in Milan) 2 nights

Why? Why would you base an hour away in Milano to spend time on a beautiful lake and where you could stay on the lake?

Rome and Pisa 3 nights

Together?

Halve the number of destinations. Moving destinations looses too much time.

Paris deserves 4 full days as an absolute minimum without any side trips. Santorini doesn't fit with the rest of your itinerary and early May is not the best time to visit there. I would imagine that it's not the easiest airport to fly home from.

I would suggest Amsterdam 3 nights including recovering from jetlag.
Paris 6 nights with a day trips to the Loire Valley and Versailles
Rome and Pisa 5 nights
India from Rome.

The train from Amsterdam to Brugge takes about two hours, not counting travel to/from the stations, waiting for train change in Antwerpen, and checking out/in at hotels. I just did this trip in reverse on the Thalys train and it was easy.

Overall I do think your itinerary is scattered, and you will spend lots of time in transit. But if these are the places you want to see, it can be done.

Look at rome2rio.com to check distances and times for various modes of transportation.

Too many cities in too few days. As has been suggested, pick your top four and concentrate on them. You want to have memories of people, place, and things rather than memories of train stations and airports. Travel rule to remember: It almost always takes longer to go from Point A to Point B than anticipated.

Your itinerary is fine in terms of transport arrangements getting you from place to place. However, It does not allow for time at your destinations to really see anything and enjoy the experience.
I think you should be satisfied spending 16 nights a bit more realistically ...

Amsterdam - 3 nights
Bruges - 2 night
Paris - 4 nights
Chamonix - 2 nights
Lake Como - 2 nights
Rome - 3 nights

I agree with David, arrive Amsterdam, stay 3 nights, to recover from jet lag. Bruges should be 2 nights, since it takes a bit of travel time to get there.

Lake Como--stay there, possibly in Varenna. Why stay in Milan and have to travel back and forth?

I don't understand Rome and Pisa 3 nights?? They are nowhere near each other. Pisa is usually done as a day trip, or as a stop on the way to the next destination. Rome should have at least 3 nights, IMO.

Can't say anything about France since I haven't been there yet.

Thanks a lot everyone for their suggestions. This has been really helpful. So to summarize, i will follow the below itinerary. I have dropped some places.

Amsterdam - 3 nights
Bruges - 2 night
Paris - 4 nights
Chamonix - 2 nights
Lake Como - 2 nights
Rome - 3 nights
(suggested by David - Thanks)
Now i remain with a few more questions.
1. In Chamonix, will the lifts be working during mid may for Aguille du midi and Helbronner and the Ice cave?
2. What is the best way to travel from Paris to Chamonix?
3. In Paris i am interested to see the Eifel tower, Lovre museum, Arc and few in city places. Since i have 4 nights what do u think should be my plan. I would love to do some countryside day trips. Can you suggest some?

Looking forward to your reply.

Thanks
Ankur

Aiguille du Midi cablecar runs year round, however Helbronner only in summer, from May 30 it appears ...
http://www.chamonix.com/aiguille-du-midi-timetables-and-rates,180,en.html

Best connection from Paris in mid May ...
1) TGV 9765 Dep 09:11 PARIS GARE DE LYON (France) Arr 11:48 BELLEGARDE (France)
2) TER84517 Dep 12:09 BELLEGARDE (France) Arr 13:56 ST GERVAIS LES BAINS LE FAYET (France)
3) TER18917 Dep 14:05 ST GERVAIS LES BAINS LE FAYET (France) Arr 14:50 CHAMONIX MONT BLANC (France)
This last train is on the route of the Mont Blanc Express. http://www.mont-blanc-express.com/cms

For transit Paris-Chamonix, you could do TGV from Paris-Geneva then the airport
Chamonix Shuttle bus. Should save 1 1/2
Hours travel time.