With five weeks in Greece you don't have to be on the go every day. A week at a time in each location sounds like a good idea, and will give you a chance to settle in and participate in local life. Personally I would pick a small seaside village near Kalamata rather than in the city itself.

With 12 days for the Peloponnese, I would personally close to split them among 2 to 3 "bases" for my day trips. Nafplio makes an excellent base for the Argolis and parts of Corinthia and Arcadia. You could then spend a night in Monemvassia and drive the Mani on your way to your next base near Kalamata. From Kalamata, you have Koroni, Methoni, Pylos, ancient Messene, and Bassae within reach. Ancient Olympia is a must see. It would be an awfully long day trip from Kalamata. Perhaps on your way out of the Peloponnese? You could take the bridge at Patra and proceed to Delphi that way? Hopefully some of the other Greek experts will chime in. There is so much to see at Olympia that it could merit an overnight depending on how fascinated you are by the ruins. The museums are excellent as well, though the modern town is nothing special. We've stayed at the Best Western Europa hotel three times and really enjoy it. Their restaurant is great, all locally sourced and mostly organic.

First of all congratulations for the early planning. You have plenty of time to get all the information required and adjust your plan exactly to your needs.

June is an excellent period to travel to Greece since it is not packed with tourists even in the most touristic locations.

I will try to answer to your questions, and also make some suggestions for you to consider.
Driving/Navigating
If you use a GPS (eg one of your mobile phone) or a map, you will have absolutely no problem.
Road signs in main roads and touristic places are both in Greek and English. In less touristic places you will find signs only in Greek. This where you will need your map or GPS. Greeks are very hospitable and familiar with tourists. A lot of them speak good English and most of them will be able to give you basic directions if you ask them.
So, you will have absolutely no problem navigating and driving on your own.

Need of car.
A car is not only unnecessary in Athens and in places like Santorini and Mykonos, it can also be a problem that could actually slow you down.
Excluding such places, a car is always a plus! It will provide you with freedom of movement and flexibility of planning. On top of that you will be able to explore and discover places that you would not be able to do with other means of transport.

Change of number of nights.
Yes I would. You have plenty of time to spend in Greece, which means you can do many things and see many different places. However, in order to be able to make a suggestion, and exchange views and opinions with you, I would like to know more about your needs, desires, activities you want to do, type of holidays you prefer, and amount of money you can spend. So, if you like drop me a mail and we can discuss more about it.

Αthens-Mykonos-Santorini
Not bad plan.
Although just using the ferries and not plane is cheaper, and if you include the airport delay times (security checks, early arrival for check-in etc) the just ferry solution is also faster.
One question if I may. Why you have included Mykonos in your plans?

Recommendations on where to stay.
I never suggest specific hotels, even if I have stayed on them myself. But I can give you some general guidelines on how to choose one. 100Euros (just a bit more then 100USD) budget/night is quite realistic for good accommodation during June in almost all locations.

I will be happy to discuss with you your trip in more detail and help you make the best of it.

Hi Dimitris,

Are you connected with the Discover Greece travel company?

I agree with those that are suggesting a shorter stay in Athens. We were just there and 2 - 3 days is more than enough especially when there is so much more to see on the Peloponnese and the other islands. Athens has limited appeal in my opinion whereas the other areas are much better for sightseeing.

All the signs are in Greek & English as I recall and just about everyone speaks English extremely well.

We stayed at Marianna Pension in Nafpoli and recommend it. I don't think I would recommend staying overnight in Delphi. We did - but had we known I think we would have gotten there very early in the day and not stayed. With the exception of the Oracle sight there isn't much else to do.

I tend to be a slower traveler than many on this forum and I always try to get a feel of a place rather than seen the major sites and then move on. I think people often under-rate Athens. Athens is a real place even on its tourist core, rather than a theme park-like historic city center that many other European cities seem to maintain. Due to historical reasons the architecture down town is not the best and there are many run down areas, but there are many different districts to explore and each one of them has a different ambiance and kind of attractions. Athens marketing is very poor too, while other countries promote even the tiniest lesser site, museum or shop, Athens world-class museums and other attractions are widely unknown. So expectations created before going and how to fulfill them differs and influence the overall experience.
I think Athens deserves at the very least 5 full days, but then it is just me, known to have spend 1 week on my first Dublin visit, ditto for Warsow and more than 2 weeks on my first London visit, ditto for Paris...

Traveling style, interests and prior research dictates here.
For example only very few visitors explore Delphi surrounding area which includes interesting mountain villages, an extended winter ski center, cute sea side villages, coves and beaches, tons of hiking opportunities and even... a mining museum one hour driving towards Meteora direction... Of course they are hardly aware even of Delphi Angelos & Eva Sikelianos museum on the upper part of modern Delphi itself, let alone all those places.....

We were in Athens for awhile, and I am just not an Athens person. I loved the ancient sites (and our daughter & her family are actually living there) but I just wasn't comfortable in the city. I love Greece (we explored Hydra, and the Peloponnese and would someday like to go back to explore more of the islands.

I do agree with mariha about Delphi. We didn't get to explore the surrounding areas as we didn't really have much info to do so. (Again next trip!) That area is gorgeous and worth branching out to see more of the towns nearby. Delphi (city) itself is very touristy.

Bookmarking

Things have changed a bit due to a time share availability in Turkey and ff award availability. Here's the almost final plan:
Istanbul, Turkey 5 nights
Fly to Bodrum, Turkey 7 nights (timeshare)
Ferry to Rhodes 2 nights (not enough I know but I messed up)
Fly to Crete via Athens, 7 nights (timeshare)
Ferry to Santorini, 4 nights
Ferry to Mykonos/Delos 4 nights
Fly to Athens

Here's where I still need help>

Arrive in Athens drive to Delphi, 1 night
Drive to Ancient Olympia, 1 night
Drive to Monemvasia, 2 nights
Drive to Navplion via Mycenae, 1 night
Drive to Athens via Ancient Corinth and Epidaurus; 3 nights

The rest is final:
Athens airport 1 night
Fly to Verona for wedding on Lake Garda, 3 nights
Fly to London, 4 nights
Fly home.

The ferries haven't been booked yet...I hope that part will work.

My big question is still on the Peloponnese section. Is it worth going to Monemvasia considering it's the only place we will be visiting in the southern section? Some say staying in the old town in magical but others say its only worth a half day. Should we skip Monemvasia and spend more time in Delphi and Ancient Olympia or another place along the route back to Athens like Navplion? How much time does it take to see the highlights of Delphi, Olympia, Ancient Corinth and Epidaurus. Thanks for your help. We're almost there.

You might consider breaking up the long trek between Olympia and Monemvasia, and stopping somewhere in southern Peloponnese. There are some beautiful coastal villages near Kalamata (e.g. Pylos and Methoni), and if you are interested in archaeological sites there is Ancient Messene. Then spend only one night in Monemvasia.

Have you checked the possibility of direct flights from Rhodes to Crete? There used to be one daily flight with Olympic Air, and another with Sky Express, but I don't know the situation for 2014. The merger between Aegean Airlines and Olympic Air may have some repercussions.

Heimall is right, Sky Express is an airline with flights from Rhodes to Crete so it wont be necessary to flight through Athens. I am sure that there wil be in 2014 also, it is a good air company!

You wonh have problem talking English, most people under 50 years old speak english and other languages. People over 50 years old will volunteer to guide you with hand-signs or to someone who talk english!

My suggestions to stay:
Chania
Archontiki Hotel (3 stars, inside the city of Chania)

Heraklion Crete
Arhontiko In Arhanes (15 kms from Heraklio)

Eat
Leventis Tavern in Chania
Monastiri Tavern in Chania Venetian Port
Tamam Restaurant in chania Venetian Port


Zisis Tavern in Rethimno
Symposium in Rethimno


You may have perfect vacations!