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PS: You probably guessed that my (and my wife's) main Turkish interests are historic ruins, great scenery, beautiful beaches and, of course, Turkish food. We are quite happy to stay at small B&B's or similar when travelling - no need for 5 star hotels.

We will pre-book our Istanbul, Izmir and 1st night at Eceabat accommodations but will take our chances at the other destinations as we wish to retain some flexibility while on the move.

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Pamukkale is best visit at sunset so you may want to stay overnight there. Next day you can visit Afrodesias. If you still have extra time, Cesme may worth a visit.

http://www.flickr.com/photos/youngadventure/sets/72157620754843776/

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My first question is why go from Izmir all the way up to Gallipoli...and then double back all that way?Would it not make better sense to pick up the car at Izmir,do the central Aegean section and then head north and return the car at Ataturk airport?You wouldn't be retracing old ground(and a 6 hour drive)and you wouldn't have to drive into Istanbul city centre either.
Or do it in reverse Ist>>Izm?
Maybe you have your reasons but that hit me first :)

For the days 9-11.Leave Ephesus by midday and drive to Pamukkale.You be there in ample time to look around a bit before dark and yes,you'd see the sunset too.
Next morning set off early to take a look around Hierapolis and leave by c.13.00 and drive down to Didem.This will take c.4 hours at a steady pace on a decent,pretty direct route.
You then have all the next day to view Didyma,Miletus and Priene before returning the car to Izmir.
Between Pamukkale and Denizli there is Laodicia worth a look at if you can shuffle time around to include an hour or so.
If your flight is early evening then you could break up the Denizli to Didem run with an overnight stop at Lake Bafa which is lovely and continue next morning to Didyma ruins.
It is only a c.1½ hours direct run from Didyma to Izmir with all three sites quite close together.Allow a couple of hours at Temple of Apollo,same for Miletus and an hour at Priene.This should be ample.

Since 2010 there have been no significant road changes in the area's you'll visit so your sat nav should still be good to use.

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Am I correct that the reason for the one-way rental is that you're getting a good price from a small, local car rental agency? That's why I do similar even if I try to make a true loop without any backtracking.

I do like your touring style--you've been mainly generous with your time allocation and you'll also be taking advantage of private transport by visiting some places that aren't so easy to access via public transportation!

Some suggestions based on my tour last year in that area:

1) Devote the greatest part of a day to get from Çanakkale to Assos doing your best to follow the coast once you are south of Troy. Geyikli will be a good as a first destination for the GPS system. Then just follow brown signs to your hearts' content as there are a great number of lightly visited and quite interesting ruins and other things to see on the way to Assos! The scenery is also quite interesting even if you rarely see the sea. Perhaps my biggest mistake in last years' tour was not devoting enough time for this short journey!

2) Take the road that runs between Bergama and the E87 a few kilometers north of Ayvalık. For reference, Aşağıbey is a town on this route. This is a good two-lane road and the scenery is beautiful!

3) No, there is no problem to visit Ephesus and then drive to Pamukkale before dark.

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As for your two "unknown" days, here is my suggestion: It does involve rural roads and some mountain driving. The roads, while small, are paved and the mountains are reasonably sized. In addition to GPS, have a Turkish road atlas--not just a small-scale fold-out map!

After the morning at Pamukkale, head to Aphrodiasis. After visiting Aphrodiasis (and I will honestly say that in many ways it is more interesting than Ephesus), enter "Tekeler" as your GPS destination. After Tekeler, choose "Selimiye" as your GPS destination. Somewhere along this route--and likely before Tekeler--you will probably want to stop for the night. You will only be going through villages and small towns and while I have not spent the night on this route I have no doubt that you can find reasonable accommodation for the night somewhere.

Once you reach Selimiye you will be on the D525, the major road that leads into Izmir. From there, Didyama is a short distance away. While I think it is slightly southeast of Selimiya (a right turn on the D525 and involving a little backtracking to get to Didyama), there is a mainly unexcavated ancient city just a couple hundred meters E of the highway with a quite nicely preserved "Temple of Zeus". While I consider it very worth a stop, you are likely to be the only tourists as it is bypassed by the commercial tours that run between Bodrum and Ephesus.

I would then suggest spending the night at Bafa Lake before returning to Izmir (and there are some more brown signs to follow) the next day.

I have driven much (but not all) of the route from Aphrodiasis -> Tekeler, almost by accident as it was chosen as the "shortest/fastest" by my sat nav system on the way from Bodrum to Eğirdir. Shortest? Maybe. Fastest? VERY doubtful. Beautiful? YES! There were a few, short unpaved stretches that while I suspect were unnecessary were no problem with a Renault Megane.

Enjoy your tour!!!! The NW region of Turkey was my last to privately tour in large part because there seemed to be not as much to see as in the rest of Turkey. I was WRONG--especially with regards to the Aegean coast in the general area of Assos! For next year I'm torn between re-visiting the NE or the NW even if those beautiful mountains and wild roads of the NE are calling loudly...

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Thanks guys for your suggestions. I like the idea of adding Laka Bafa & Laodicia to the itinerary and will shuffle things around to see if that's achievable.

I was reticent to choose Istanbul-Eceabat on the first day. This is because in 2010 our sat-nav had us driving around in endless loops and onto dead-ends all around the airport! .....I might just need a better sat-nav?!!?

It may be possible on day 1 to fly from London-Istanbul then drive to Eceabat. That would free up one day.

The additional cost of one-way car hire trades-off against not having to double-back. Need to check prices. Any recommended firms?

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Ar least you're only flying in from London not Aussie so jetlag won't be an issue :) It will take you 6 hours at a steady pace to reach Eceabat so if you land before lunchtime this is a good option.
If later then consider looking for a good connection to Izmir and do your route in reverse.
A hire company I frequently recommend is www.economycarrentals.com because they are reliable and have nationwide coverage.Remote drop fee's are included in the prices when you look on their web site,yet even with this included they are still consistently cheaper than most other hire companies.The price difference between petrol and diesel models is also negligible.

Archeologists are still working at Laodecia so you may not be able to view everything there but it is still worth a peep and Lake Bafa,village of Kapıkırı is lovely.Plenty of nice places to stay there although there are no über cheap ones.

I don't know why your satnav did that to you(but then I don't trust modern technology!)but the signs out of the airport are pretty clear-trust your eyes not the satnav :) ,just follow signs for Tekirdağ and Edirne initially (plus the more local Silivri and Çorlu)and then you'll start to see signs for Çanakkle,Eceabat etc.,.