I thought the web site limited you to eight segments for E-Tickets, and UC 3.0 also imposed an eight segment limitation.
I've had a similar experience with the web site; it usually fails to price "micromanaged" itineraries. I tend to do much better specifying every other place I want to connect, and letting it fill in the blanks.
I don't like having superfluous humans in the loop. I ran into "but there's a nonstop available" coming back from the Catman Do. I had to explain to the check-in agent at JFK three times that I really wanted to fly through Los Angeles. (JFK-LAX was only about half full, and the LAX-SFO segment ended up departing with two empty First Class seats; I don't know why the agent was being so pushy.)
I haven't encountered a competent travel agent in many years.