If you want to og to Turkey specifically to visit Troy,you should fly to SAW airport,which is on the Asian side,and not IST,it is also generally cheaper,and served from Athens by turkish LCCs. From there you should rent a car,its a couple of hous drive.If you find a morning departure and a return the next day its easily done in 2 days.Car hire is not very expensive in Turkey,but gas is 10bucks a gallon.

If on the other hand Your interested in archeology and want a 5 day trip you could do this.

1 Day to Troy.
2 Day afternoon to Ayvalik to have a great fish dinner right by the sea,and say helo to my house,offcause!
3 Day,morning or early afternoon to Bergama and on to Izmir,that Depends on the amount of Raki you enjoyed with your Cunda dinner ofcs.
4.Day to Ephesus.

This is an easy trip withouth long driving days,although I do not know how one way rentals work out in Turkey. It should also be doable on public transport,by bus,i do not know how to get from Hisarlik to Ayvalik(or anywhere else for that matter),but the rest are trips of 1 to 2 hours by bus,and there are busses evry hour until quite late at night.

Returning to SAW from Izmir ADB there are flights for something like 20-30 usd.

Sorry,a bit embarasing,it would take abouth 5 hrs to drive to Hisarlik,actually pretty much the same from IST or SAW.Looked at wrong Hisarlik.From IST,I do positively know that the easiest for Canakale is a ferry from Yenikapi to Bandirma.
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