I am planning a 2 week trip for 2 in Greece in late September-early October with the following rough sketch of days:
Athens 3 days
Cyclades 3 days
Peloponnese 2 days
Delphi/Meteora 2 days
Thessaloniki 2 days

Is there a travel pass that will help cover the costs of museums, archeological sites, etc. akin to the English Heritage pass or Turkey Museum pass?

Renting a car from the airport - is Athens navigable by car or better walk/use public transportation alone? We were planning on taking the car for the Cyclades which would mean a bunch of ferries with the car on the islands, and then of course car for all the rest of the trip after the islands. What about tips for the ferries? Do I need to book ferry rides well in advance if taking a car?

The big question for me is if the car could be useful for Athens. One thought was that it could be a good thing if we take a day trip or two to Sounion or Epidauros.

Any beach or restaurant tips in this itinerary? In particular, any places recommended to stay in the Cyclades (2 nights there)?

This will be a lovely time of year, but a gruelling itinerary during which you will see almost nothing but highway and ferry boat windows. What are your true must sees?

I've been told the same for recent Italy, Turkey, and England itineraries and that was not my experience. While grueling I definitely did take in the places and it was not all highway or ferry. The islands are a must for my travel partner but she also wants to see historical sites obviously. Food is less important i.e. lunch is not mandatory and later dinner is OK.

Epidauraus is in the Peloponnese.

Given your itinerary, I would lose Thessaloniki.

I wouldn't keep a car while in Athens, even if it is to drop down to Sounion. I used a car to go to Meteora and Delphi and kept the car to visit Sounion. Only then did I return it to Athens. Before hitting the Temple of Poseidon, I also went swimming in Lake Vougliameni which is an awesome site. Open year round as it is fed by a hot spring. That would be my 'beach tip.'

IMO, a car would be a distinct disadvantage in Athens. The Cyclades, too, for that matter! If you want a car while on one of the islands, use a local option for a one-day rental.

I agree that this itinerary is seriously rushed. 3 days is barely enough to scratch the surface of Athens. 2 days is short for the Peleponnese. 2 days for both Delphi and Meteora has you on the run. I’m not sure how you are estimating driving times, but FWIW, the estimates I got from google maps were too short, even if I entered the correct day and time. Try adding 25%.

I travel much faster and harder than most people and I also skip lunches and eat dinner late; I would not attempt this itinerary. I see that you believe you can do it. Have you plotted things out on a calendar?

And if you do stick with this itinerary, why start with Athens? It would make much more sense to start with the Cyclades.

If you haven’t seen it, here’s my trip report. The section on the Cyclades begins with post # 89. With Gratitude for a Glorious Solo Month in Greece

Hope that helps!

Yo Treb, superb advice from all above.
I am done. the olives

Athens by car is the hell. Most touristic places can easily (and faster) be reached by metro.
The metro between the airport and the city runs every 30 min and the railway (more or less same itinerary) every hr.
A car may make sense if you plan to go from Delphi to Meteora and then to Vergina - Thessaloniki.
Thessaloniki can be reached by plane (direct flights) from some cycladic Islands too.
As to the Peloponnese, define the places you want to visit and then calculate the time you will need for that.

So I reworked things to the following:
3.5 days in Athens sans car - pick up car shortly before leaving Athens
Ferry from Piraeus to Santorini and visit 1 day
Ferry to Naxos and visit 1 day
Ferry to Mykonos and visit 1 day
Ferry to Delos and back to Mykonos and then from Mykonos another ferry back to Rafina 1 day
Peloponnese x3 days to see Nafplio, Corinth, Epidauros, Sparta, Argos, Mycenae, Mystras, Olympia, ?Patras
Meteora +/- Hosios Loukas 1 day
Delphi 1 day and then drive back to Athens area
Fly out next day

So, dropping Thessaloniki opens up a bit more time for Athens and the Peloponnese

Are there tips on a travel pass or travel card recommended that helps cover attraction prices?

Any tips on a central location in the Peloponnese that would enable day trips to the above mentioned areas and also allow us to not have to switch hotels every day?

Adding a bit of time to Athens and to the Peloponnese makes sense from my perspective. That said, sorry, but I'm not seeing the time for transportation in this revised plan, and it seems to me you have a lot of time in transit for very little time in the places you stop. JMO.

An example: The ferry from Piraeus to Santorini takes a minimum of 5 hours. All for one night on Santorini? Maybe I'm misreading....

If you are trying to reduced the number of changes of hotel, consider visiting Delos and Mykonos from Naxos, though I don't think that option is available every day.

I would be hard pressed to visit Meteora and Hosios Loukas on the same day. YMMV.

Also: Why not start in the Cyclades rather than Athens?

Peloponnese:
every place you mention except Olympia can easily be visited in day trips from Argos or Nafplio. The latter is the nicer ploace.
You may also visit Corinth (Akrokorinthos) on the way from Athens to Nafplio.
A day trip from Nafplio to Olympia isn't impossible but it's a very long ride though the mountains.

Peloponnese - Delphi/Ossios Loukas - Meteora:
There is no really fast itinerary.
Either via Rion-Antirion bridge or via Isthmia - Elefsina

kja made a good proposal:
fly from your home town to Santorini (with a plane change either at Athens or somewhere else in Europe).
Poceed then by slow ferry (stunning views of the caldera) or catamaran to Naxos and by catamaran to Mykonos.
The bus system on the Islands is rather good; I don't think that you will need a car there. Otherwise check wether a car rental just for the day or a taxi ride is the better solution.
Visit Delos in the morning and proceed in the afternoon by ferry to Rafina where you sleep at hotel Avra.
Take then the free hotel shuttle to the airport, rent there a car and go on to Trikkala - Meteora.
Backtrack up to Lamia and proceed to Ossios Loukas - Delphi and then either to Rion bridge or to Elefsina (as above).
Stay the last days in Athens (ferries may fall out because of rough sea or strikes).

Neckerd has done you the great favor of planninig the best possible itinerary, with experienced tips on best transport options ... and unlike travel agencies, doesn't try to "upsell" you into needless high-end hotels, car rentals or unneeded "transfers." Do yourself a favor & adopt this itinerary and thank him for it! When you've got your arrangements locked in, we can address lodgings.