I also feel this way about expedia which I have actually tried to book on, and every time I get to the credit card info, get bumped out of the system
I've made one booking Expedia and it was easy. They couldn't do it eticket (it was an interline fare between US and UA), and the ticket arrived promptly just a few days later. They automatically assigned seats, and, much to my joy, the UA seat was in Economy Plus even though it was a discount fare and no status!
My big complaint, and the reason I don't use it, is that you can't see connecting times in the flight listing screen. They simply show departure time/arrival time and connecting point. So I've found a perfect flight, and selected it, but by the time I get to the flight details screen, I see that I am left with 35 minutes in ATL, and that's too short for me. They really should display all flight times on the listing screen, and not just the origin and destination times. While they're at it, put in the aircraft type there too. I like to see my aircraft options!