UA.com does actually bias display of "through flights" (e.g. same flight number) over similar "connecting" (change of flight number) itineraries with similar total travel time and cost, the actual display is also different (IIRC, displays it as "1 stop" vs two flights)... I somewhat recently was looking at a XXX-CLE flight and got very excited initially that it was on a 757-300, which hasn't seen revenue service to CLE in quite a few years, but it was only when I looked very closely that I realized it was something like IAD-MCO-CLE with the same flight number and a change of gauge in Orlando (757 IAD-MCO, 73-something MCO-CLE)

But even WN, IIRC, is moving away from truly direct flights