I agree a lot of the 'options' are purely designed to increase revenue whereas if you accept the automatic selection it seems intent on inconveniencing you.
I used to work for a Big Company so I took flights mostly on my preferred airlines. Now I have to shop for the best deals - I often find by going direct to the airline, comparing with say Zuji or such - I can get good enough deals on the traditional carriers at least as good as the LCC - but without all the LCC hell. But - it means sitting at the 'puter - sometimes over several days & with my (little) knowledge of routes / times to get a nice deal - something a lot of people just can't or won't want to do.
What does surprise me is when flitting back & forth from site to site the prices can vary quite considerably with one airline. I'm sure there is a good reason ;-/