Many of the travel company in Turkey organise guided package tour with a big group. But most of the traveler are looking for part of individual and part of organised tours. Travel with public transportation (Bus, train, plane or ferry) and a day trip in the area with a local company. These tours are given you a chance to meet other people from diffrent countries. After tour you will get free to explore city with your partner or friend. Some of the travel agent organise for you individual tours in Turkey. In advance you can book your accommodation, Transportation, daily tours and airport transfers to your hotel. So you dont have to fallow a guide with 40 other people. A few reccommended travel Agent in Istanbul :

Zais Travel Agency
Rutas Turquia for Spanish Speakers

Better use a travel agency in Turkey for domestic flight booking, bus, train or ferry tickets, hotel booking, rent a car and daily tours. They can organise your travel needs while you are sightseeing in Istanbul. You can save your time and money. Most of the travel agency has special rates from hotels, bus companies etc. and they offer you a better price than you get on your own. If you dont like to use a travel agency at least visit one of them and get a free travel information. Turkish travel agents are not charging anything for information about Turkey travel.