Admittedly I have limited experience with this, but it really isn't difficult to work around once you know it is a problem. Since this first came to my attention (thanks FT) if while I'm booking a flight it comes up as direct with a stop I just start over and use the "more search options" to separate the two segments. I have a BDL/ATL/DFW coming up later this month where I did this when I booked the flight.

I compared the price as two segments and as direct with one stop and there was no difference. YMMV of course.

It would be nice if we didn't have to do it this way though.