I guess I'm in the minority on this one, but I love the 5K and 10K route for Marathon Weekend. I wouldn't be against them mixing it up, but I don't think they are bad courses by any stretch and you don't get to run in the dark with the torches lit in the later races (at least I don't, maybe the Elite runners do). It certainly feels like a much different experience than Epcot during the Half (I barely consider what the Half does as running in Epcot) or the full (later in the day, while the park is open, in most cases). I understand how it could become a little boring for return runners, but for first-timers they are both amazing courses IMO. When I talk to people who aren't looking to run a Full Marathon I lean heavily toward recommending the 5K and 10K over the Half because the courses are so much nicer. I mean MK is cool and all, but 13.1 is a long distance to cover where that is the only highlight.
ETA: I can definitely see how running both the 5K and 10K in one weekend can feel redundant since they are so similar. It doesn't bother me because I love Epcot, but if they were to move one of the two races to focus on another park (preferably the 5K) I wouldn't complain.