Please, don't forget to come back and write your trip report. I want to do the same trip in the future, including Cappadocia.

I definitely will.

Our schedule is:

10/8/2012 Air
10/9/2012 Istanbul
10/10/2012 Bodrum - Macakizi
10/11/2012 Bodrum
10/12/2012 Bodrum
10/13/2012 Bodrum
10/14/2012 Rhodes - Lindos Blu
10/15/2012 Rhodes
10/16/2012 Rhodes
10/17/2012 Rhodes
10/18/2012 Crete, Agios Nikolaos - St. Nicolas Bay
10/19/2012 Crete, Agios Nikolaos
10/20/2012 Crete, Agios Nikolaos
10/21/2012 Crete, Chania - Casa Leon
10/22/2012 Crete, Chania to Santorini - Katikies
10/23/2012 Santorini
10/24/2012 Santorini
10/25/2012 Santorini
10/26/2012 Istanbul - Ibrahim Pasha
10/27/2012 Istanbul
10/28/2012 Istanbul
10/29/2012 Istanbul
10/30/2012 Istanbul

For boat rides or winding mountainous roads, bring something to help with motion sickness if you are at all concerned. I ran into rough mediterranean waters in late September 2 years ago, and the 30 minute large ferry ride felt like an eternity. The following day all boats serving the almafi coast were cancelled. Better safe than sorry on your honeymoon! Have a great time!

Is there anything in particular you recommend for motion sickness?

Our two ferry trips are from Marmaris to Rhodes and Heraklion to Santorini.

I am happy that you will be staying in Chania as I read your interests, and beauridul, historic Chania fits them perfectly. Have a wonderful trip.

Sfgvacas, Congratulations; Your itinerary looks good to me.
In Rohodos my favorite is Melenos Lindos, however I had guests stayed at Lindos Blue as well and were happy.
Katikies in Oia is good choice as well but other options were good too. Make sure to dine at the Amoudi beach just bottom of where you will be staying.
St. Nicholas Bay is good place as well, Nicos will be happy to help honeymooners. Ag. Nicholas and Elounda are the upscale part of the island anyway.
In Bodrum pay a visit to Gumusluk area for a romantic dinner by the water, hope weather will be gentle. Generally speaking daytime will be gentle evening might get a bit chilly.
Happy Honeymoons,
Murat

I think it's a pretty good plan for having rest, but if you want more active holidays you should add something in this list

Thanks everyone!

Jozeph:

Could you expand on your thoughts?

The post by troubadour59 is one of the most biased I have seen on Fodor's. Could it be because he is in fact the owner of the hotel he recommends? :-D

Exactly Right. Good catch, Don! Look here: http://www.ttgmena.com/Mandarin-Bout...walking-weeks/

Heimdall if you knew know both location, I am sure you will agree with me......I know this part of the world for over 40 years, and beside nightlife in Bodrum, a castle and a small amphitheatre, there is not much more to see, unless you like the nightlife and the jetsetting...
Brotherleelove, if I want it to hide I could very easly therefore I dont think you are right in saying a "good catch"

troubadour59, so many days in Fethiye are too long, i would suggest skipping it , and add all these days to Greece.

"Avoid Bodrum".......I have been to Bodrum. I was there for 10 days and did not get bored. There is much to see and do and using the bus/dolmus system you can visit lovely seaside villages such as Gumusluk.

"3 days in Rhodes is too long".......NO, it is not. Rhodes is a very large island and it takes at least a week to explore it.

"4 days in Santorini is too much".......NO, it is not. There is much to see and do around the island and it takes at least 4 days to relax and enjoy it. I go there for up to 4 weeks and I don't get bored.