Greece Itinerary 9 Days

Two nights somewhere is one full day, so your trip is rushed. Personally, I would drop Santorini (too Disneyfied these days) and add a night to Athens and to Chania.

I haven't been to eastern Crete, but I have read that it is beach-resort-and-party land. Most sources indicate that the western part of the island has more non-beach sightseeing attractions. I hope others here can comment on Elounda specifically.

If I had just 9 nights for all of Greece, I would not spend 3 of them at Elounda. Then again, I am not interested in beaches in general.

You have too little time for this many locations.

Personally I think Santorini is a must see destination for first time visitors. Indeed it is very expensive and can be crowded with cruise ship people but the views are spectacular. Your two nights in Santorini is really just under a day and a half. I would be tempted to add a night to Santorini. Thats my normal time for Santorini. Its all my budget can stand.
Santorini http://www.flickr.com/photos/stanbr54/sets/72157632154800782/

You will have to take the ferry to Heraklion Crete and the ferries don't get to Crete until about 7:30 in the evening so you have to make a decision about where you want to spend your time. Do you stay in Heraklion for the night or try to get to your next destination. You probably have just enough time to catch one of the late buses to Chania as the bus depot is close to the ferry port. It is a 2.5 to 3 hour trip.

Because Elounda is in the east and Chania is in the west you are gong to use a half day minimum getting from there to Chania. Thats a waste of time and short changes both locations. I would drop Elounda and concentrate only one location and that would be Chania.

There is lots to do in West Crete. Stay in Chania old town. Time is standing still in the old town its amazing. You are going to need 2 to 3 nights to fully explore Chania which really only gives you 1 day to visit one of the nearby sites. Ancient Apter is a good choice or even better is the day excursion to Gramovossa with its pirate fortress and beach plus the famous Balos Lagoon beach. My plan will give you a glimpse of what Crete is all about.
Chania http://www.flickr.com/photos/stanbr54/sets/72157632117917828/

Gramovossa, Balos Elafonissi https://www.flickr.com/photos/stanbr54/albums/72157698932695812

Ancient Aptera, Melidoni Cave and village.

https://www.flickr.com/photos/stanbr54/albums/7215767211837963

And just to add a clarification you can take a ferry from Santorini to Rethymnon on Sat and Tuesdays. It will be a seajet. Rethymnon is only an hour commute to Chania. Just one word of warning you will have no more than 20 minutes to get to the Rethymnn bus station for the 8 PM Chania bus. The taxi drivers at the port do not want that trip and will refuse to take you because its only a 7 euro fare. Plan to hire a private transfer company to meet you at the port and take you to the Bus station. Alternatively have a 20 in you hand to persuade the taxi driver to take you.

Thank you all for your responses, very helpful information. Agree with 2 night stays not allowing time to see much. Less is more!

In my opinion, Santorini is a must with a minimum of three nights. We stayed in Firostefani at Lithies Traditional Homes where the sunsets were gorgeous and the crowds were not massive like they were in Oia. Our trip began in Crete and we preferred Eastern Crete to Western; staying at a B&B near Vamos. I can't speak to Elounda because we did not visit there. If you are at all interested in wine, then Dourakis Winery is not too far from Chania. They have a fabulous tour and light lunch that is very reasonably priced. From Crete we took the ferry to Santorini. You will love Greece!

Two nights can be enough in Santorini -- a couple of good sunsets from a cliffside hotel or restaurant in Firostephani (avoid Sunsets in OIA - it's a zoo -- check out this photo montage: http://tinyurl.com/lnquk6h). On your first full day rise early & catch the First bus to OIA, get there before 9 if possible, and you'll have 90 minutes in which to wander & take good photos before the huge throng of cruise-goers jampacks the narrow lanes to the brim (see this photo montage of OIA at sunset & before: http://tinyurl.com/lnquk6h). When crowds arrive, you hop bus & leave... go to Fira Museum, small & good... maybe Akrotiri "dig" if you've read up on it & have good info. A good sunset dinner place in Fira is STANI, topfloor roofed terrace, they'll reserve good table view free (I stop by earlier & choose exact table), and give you a fine traditional Greek meal including wine for no more than €15-20 each. Walk the rim path back to FIrostephani ... it's "hidden" because tour groups don't stay there, their busses zip right by. You don't need to do food or wine tour, you have loads of time to do this in Crete.. without crowds! Ferry on day #3 leaves 5:30 pm