In my experience booking THY domestic flights through expedia will only show up the full flexible Y class fares. These are considerably more expensive than booking directly at www.thy.com

You won't be able to avoid the ticketing charge whoever you book with, they are still all E-Tickets it's just another surcharge.

Where are you going in Turkey? There are a loads of low cost carriers so shop around the LCCs to compare fares.

THY has top notch catering, both on international and domestic flights (though no free alcohol on domestic flights!) and I'd recommend them.