Istanbul - make sure that you pay for your taxi to Hagia Sophia in TURKISH LIRE not euros as there is no parity between the two currencies and you will be relatively ripped off in Euros. And make sure you get a taxi from the proper rank outside the ferry terminal and not one just cruising hopefully. It should cost a MAX of 20 YTL to get there, but be aware that the driver will try his luck in getting you to book a full tour with him or say he can't get quite there and drop you off 'within walking distance'!
Once at Hagia Sophia, the Underground Cistern - very unusual - is literally across the road, Topkapi Palace round the corner, and the Blue Mosque just opposite when you cross the gardens; do try Gözleme pancakes and hot corn on the cob from the vendors if you can.
After visiting the Blue Mosque, you can head up hill - about 10-15 mins to the Covered Bazaar and then steeply downhill back to the waterfront and the Egyptian (spice) bazaar. Then it's just a case of crossing the bridge and heading back to the ship ... possibly further than you think because you'll be quite weary when you return after all that walking!!
Canakkale OK sea front with model of Trojan Horse ... good for photos, because Troy itself only has another model -not surprising!- and the remains are rather hard to imagine as a great city. You can get a boat to the Gallipoli peninsula easily - about 4O mins max crossing time to Eceabat, and there are local operators offering battle site tours which could work if you are there for the day. Check on the internet for operators before you leave, and book in advance.
There is a good historical museum, but it's probably too far away to walk in Canakkale.
Kusadasi is a town that loves tourism ... the seafront is full of bars/pubs/souvenir shops. There are some beaches but they aren't particularly central. Kusadasi is the jumping off point for various worthwhile visits - Ephesus, The Virgin Mary's House, the Asklepion and St John's Basilica in Selçuk (a 'real' town with a good market, real Turks and storks!). Further afield, there's the hill village of Sirince which makes good wine, and also a good living from the visitors as every house is a shop of some sort. I saw real genuine fake Rolex watches advertised as such when I visited!! Another, less obvious place to visit is the Railway Museum at Camlik, which has loads of steam locos that you can climb all over, Ataturk's personal carriage including his bathroom with bath and wc, a good restaurant and a traditional pottery. I think it's unlikely that a cruise line would offer an excursion here, but you could see if a local travel agency could do it, or even a local taxi. But you may not be the steam train enthusiast that I am, and if the weather is good, you might just enjoy some Efes beers and the beach!
I think that you could do most of the excursions from Kusadasi privately - there may be more information on the Cruise Critic forum, because American guests in particular like to get local agencies to take them around. Of course you will have to insist that you don't want to visit any carpet factories or leather goods stores unless you really want to buy something because this is where many guides make their money, and it eats up valuable time that you might prefer to use in seeing something else.
If you decide to visit Ephesus under your own steam - and it is wonderful - bring water and a hat because there's no shade, (and beware that the stones can be very slippery to walk on,) make sure you pay for the Terraced Houses with your entrance ticket or bring money to buy an entry ticket as you pass them, and ask to be dropped at the NORTH gate and be met at the SOUTH gate as this is the downhill route and far comfier because you are not trying to fight against the tide of tourists in this direction if you decide to walk in the other direction!
