I guess that even more important than the course itself is the weather.
I have been to WDW during marathon weekend (early January) twice times now. Both times it was unseasonably cold. This year it was below freezing and sleeting for almost the entire run. I saw reports about lizards freezing and falling out of trees. Not the best weather to run it. Especially after you've finished and you are suddenly hit by this bitter cold as your body temperature dropped.
California on the other hand was beautiful. It was overcast for almost the entire run, nothing to complain about there.
The Expo was my biggest complaint about the Disneyland run. In WDW the Expo is held at the Wide World of Sports. Getting there is a breeze from any Disney resort and there is more than enough room (not to mention parking). There are 2 rooms, one for picking up your number and another for Disney Marathon Merchandise and Third Party Vendors.
Disneyland in my opinion was a nightmare. I did not receive the email saying that the Expo would be held at the Disneyland Hotel. I asked a Cast Member who told me it was at the Anaheim Convention Center. So I walked the mile there to find out that it was in fact not being held there. I called other people who were running it and they and no clue either. I walked past the convention center on the back side of California Adventure towards The Disneyland Hotel. There were no signs about the expo!!! Finally we found out it was at the Disneyland Hotel. So we went to the convention center area and were told we had to pick up our numbers before we could go in the convention area. And where were the numbers you ask? On the bottom floor of the parking garage obviously. They only had signs on one side of the hotel (which was not the side I came in). Picking up your number on an astro-turfed parking garage is not all that great but I guess it's all they have to work with. The convention area was nice but probably half the size of WDW so walking around was kind of a nightmare.
We have an obvious winner here: WDW
Next time I'll show you the medals, these change every years though so don't pick your run based on them.