Planning Your Time
You can see a bit of the Sea of Marmara on a quick one- or two-day trip from Istanbul: you could do just a day in İznik (make sure you leave Istanbul early), but you'll want to spend a night, at least, in Bursa. The ferry from Istanbul's Yenikapı terminal to Yalova takes about an hour; from there, you can catch a bus to İznik or Bursa. There are also direct ferries to Bursa (Güzelyalı) from Yenikapı, though you should allow an hour to get between the ferry terminal and the city center by public transportation.
An optimal way to spend two days around the Sea of Marmara is to leave Istanbul by ferry early enough to be in Yalova by mid-morning, then catch a bus or drive to İznik and have lunch by the lake. Next, head into the center of town to visit the Saint Sophia, the Lefke Gate, and some of the famous tile workshops. If you leave İznik by late afternoon, you'll be in Bursa in the early evening. Spend the second day sightseeing in Bursa—don't miss Yeşil Cami, the covered bazaar, Ulu Cami, and the Muradiye Tombs. For lunch, make sure to try the İskender kebap. If you have time, you can take the gondola lift up Uludağ and enjoy the view from the mountain’s pine-covered slopes. Head down to the Bursa ferry station in the early evening and catch the last boat back to Yenikapı terminal in Istanbul.
You can visit Gallipoli in a long, rushed day trip from Istanbul (as many tour operators do) but you’re better off spending the night in Çanakkale and seeing the ruins of Troy as well. If you have five or six days, you can pretty much see everything in the vicinity, visiting İznik, Bursa, and Çanakkale, then continuing on to Behramkale (Assos) and Ayvalık, with a visit to Cunda, Ayvalık's main island, and the ruins of Pergamum. Be warned, though: Once you get a taste of the area’s natural beauty and relaxing vibe, you might want to stay longer.