On what route are you flying?
I flew STN-SAW-BOD last summer on Pegasus, and found the experience perfectly pleasant for an LCC. The connection time at SAW was tight even before considering a slight delay (we practically ran for the gate and were amongst the last on), but the flights were fine. We brought our own food and water. The safety video was extremely funny, which actually made one watch (and I fly several times a month).
While I did not fly AtlasJet, I did fly OnurAir BOD-IST. It may just have been the domestic flight, but Pegasus was far preferable. OnurAir had few non-Turkish passengers, and little English was spoken by crew. Pegasus felt very much like an efficient LCC, such as EasyJet or AirAsia. While I did not fly them, AtlasJet was extremely efficient in cancelling and refunding a ticket I had purchased prior to finalization of the itinerary.