Mom+daughter Two Weeks first time trip to Greece

Looks good. You've given yourselves enough time to enjoy and relax at each destination. I do recommend that you fly to Santorini to save some time. From Naxos you can fly or ferry back to Athens.

Why do Hydra??? That is an island constantly promoted by R Steves mainly because his tours don't cover any other islands. If you see Santorini & Naxos, Hydra will be a big nothing. Instead, do not do a day-only trip to delphi, take a KTEL (intercity) noonish bus up t o delplhi, enjoy some of the ruins befoe sunset, stay overnight, see museum & rest of ruins in AM, then bus back... MUCH more enjoyable than rush-rush-rush day trip (3.5 hour on road EACH way -= 7 HOURS of day in transit). Take it from someone who has experienced both. If you are worried about what your hotel will say, Dont worry... just tell them you're gong to be away 1 night ... they will hold your big luggage in storage room for that 1 night. Believe me; have done this sort of thing many tmes. Athens hotels are used to people doing a "night away" thing for tours.

I might be tempted to drop one night from Santorini and add it to Naxos. Naxos will give you a more authentic Greek experience.
I also agree with Lee, fly to and from your islands . Make the Santorini to Naxos your ferry experience.

And Jans comment about doing an overnight in Delphi will give you time to visit the museum and perhaps the lower site which has no gate and is open all the time. Next morning you will have the main site pretty much all to yourselves. When the tour buses arrive you can leave and catch the next return bus to Athens. This plan maximizes you experience.
Here is what you can expect.
Nafplio and Peloponnese http://www.flickr.com/photos/stanbr54/sets/72157632094108982/
Santorini http://www.flickr.com/photos/stanbr54/sets/72157632154800782/
Naxos Town http://www.flickr.com/photos/stanbr54/sets/72157632094558042/
Trip around Naxos http://www.flickr.com/photos/stanbr54/sets/72157634605629689/
Athens http://www.flickr.com/photos/stanbr54/sets/72157632121475515/
Olympia Delphi Meteora https://www.flickr.com/photos/stanbr54/sets/72157645469717811/

I have nothing remotely approaching the experience of Janet and Stan with Greece, but I'll join in their recommendation to overnight at Delphi if you can. The ruins are best early or late in the day when the crowds are gone. Sunset/sunrise over the valley and the gulf are magical.

I also think you're right to spend some time based in Nafplio. Besides Epidavros, consider a day trip to Mycenae, a stunning ancient hilltop site. You could visit both in one busy day.

I think Hydra is a good choice for an island experience if your trip doesn't take you to other islands -- but yours does. So I'd give that time to Delphi or elsewhere.

I would drop a at least a day from Santorini and add it to Naxos, a much more traditional and less touristy island, especially off season for September. Even September on Santorini will have huge cruise ships depositing hundreds of tourists at a time and there'll be a number of cruise ships which will add up to thousands of tourists storming Santorini, driving up prices and adding to the congestion and losing every reason why you want to go to Greece.

I would add eliminate Delphi (while special is a difficult and roundabout way to get there). Hydra, while one of Greece's nicest waterfront is a bit over-the-top touristy but may be OK for a day trip.

I would spend more time in Athens which has some of the best World-Class archeological sites, museums, the Plaka, Monistirake & Sygtagma Square, Central Markets, Psiri District, Anafiotika, Changing of the Guards and so much more.

Hydra, while very picturesque with the best feature being no vehicles allowed on the island (other than municipal services) is very popular with jet-setters, day-trippers and very expensive for an over-night stay, could be dropped.

Delphi, while very special tends to take up an entire day, just getting there and returning so could be eliminated.

If it was me:

Nafplio: more time there
Naxos: more time there
Athens: more time there

Drop Hydra, Delphi and Santorini (use those extra days for longer stays in Athens & Nafplio) off-season will give you a wonderful opportunity to experience Greece, the more traditional and non-touristy Greece.

Nafplio is one of Greece's most loveliest towns with a nice waterfront, beautiful Old Town, archeological/historic sites right in town and great base to explore Epidavrous, Mycenea, Tryns and other spectacular parts of Ancient Greece. If you really want to see Hydra then there is a day cruise from Tolo (a short distance from Nafplio) which will give you a nice day trip to Hydra & Spetses. Hydra is far better than Spetses and will at least give you a "taste" of what upscale, jetsetters go to Hydra for.