Tours

I would want to see Istanbul and then do a side trip to the ancient site of Troy and Ephesus. This travel writer has a good article on visiting Troy. For a tour from Istanbul, she recommends this GetYourGuide tour (4.5 star rating on 81 reviews). Note that they only pickup from hotels in the Taksim and Sultanahmet areas of Istanbul. There is also a GetYourGuide 2-day tour from Istanbul that includes Troy and Gallipoli (5 star rating on 4 reviews). If staying in the area one of the best hotels is the Iris Hotel, Canakkale. There is a one day tour from Canakkale to Troy and Gallipoli.

Here is a list of tour operators in Turkey.

I love looking at Roman mosaics and the Zeugma Mosaic Museum in the city of Gaziantep in south-eastern Turkey is a must see though it is beyond all the organized tours that I've seen. The city is quite far from most tourist sites and tours, so the easiest way to get their is to fly to Gaziantep Airport (GZT), about 1½ hours and costs about $400.

G Adventures has their 15-day Absolute Turkey tour for from $2,481 to $3,039 (double occupancy) depending on the season.

TourHub has a 14 day Turkey Discovered tour visiting: Istanbul, Gallipoli, Troy, Pergamum, Kusadasi, Ephesus, Parmukkale, Fetheiye, Antalya, Konya, Cappadocia and Safranbolu. From $3,442.

Rick Steves has a 13-day Best of Turkey tour held throughout the year, averaging approximately $3,200USD.

G Adventures 15-day

TourHub 14-day

Rick Steves 13-day

Located about 40km east of the city of seaside town of Antalya, the Roman theatre of Aspendos is the best preserved ancient theatre in the world. Excavated in the 19th century it is remarkably complete.  GetYourGuide has a few excursions to Aspendos. One tour included Aspendos and two other Roman sites: Perge and Side, and a famous waterfall at the Kursunlu Waterfalls Natural Park.

Another interesting place is the ancient city of Aphrodisias. Important sites are the Sebasteion (which was only discovered in 1979), a huge Roman temple built around 60AD. Also see the stadium, the Tetrapylon temple, the Bouleuterion (a small theatre designed for political meetings), and finally the Aphrodisias Museum. Located near the town of Geyre in the Karacasu/Aydın. This website has details.

Getting there: If you are in Pamukkale and Hieropolis you may be able to find a tour operator (try GetYour Guide) running a day trip to Aphrodisias. In the high season these usually run daily.

Staying there: The nearest hotel to Aphrodisias is the Antatolia Hotel Geyre, which is about one kilometer down the road from Aphrodisias. Also the Afrodisias Otel.

The Anatolia Restaurant is a five minute walk west of the site entrance. Also see the Afrodisias Restauran (sic).

Aspendos

the Sebasteion

Tetrapylon

Aphrodisias Museum

Accommodations

If staying in Troy and Gallipoli area one of the best hotels the Iris Hotel, Canakkale. There is a one day tour from Canakkale to Troy and Gallipoli.

Iris Hotel, Canakkale

Sphendon Hotel, Sultan Ahmet, Akbıyık Değirmeni Sk. No:44, Istanbul (suggested by Sam of Australia)

Troy

My top site to visit in Turkey is the ancient city of Troy which today is near the town of Hisarlik. The town of Canakkale might be a good base because it is close to Gallipoli and not too far from Hisarlik.

Troy VII is often associated with the Troy of the Iliad

Beginnings

My blog to organize information on travel to Turkey. Sites that I want to see:

Istanbul (Hagia Sophia, the Blue Mosque)

Ancient Theatre at Ephesus

Gallipoli

Overnight train from Ankara to Kars on the Doğu Ekpresi (Eastern Express)

İshak Paşa Palace (3 hours south of Kars)

Troy/Hisarlik:

Easiest transport to Hisarlik from Istanbul is by ferry then bus then taxi - see Rome2Rio. 

Troy Museum, 8:30-19:00, 1 Apr to 31 Oct; 8:30-17:30, 1 Nov to 31 Mar. Entrance fee - 42 TL (~$3).

Hisarlik Hotel, Tevfikiye Koyu Intepe, Canakkale Turkey. Good reviews on Tripadvisor (avg. 4/5) and a 10 minute walk from the ruins - $49.