Look at it this way. Multi-window is only available on a very few devices (I think Note 2, Note 3, and Galaxy S4). Consider how many other android devices are out there besides these. It doesn't make a lot of sense for developers to spend the extra time coding for Multi-window if it's only available on a few devices (and all from ONE manufacturer). I think multi-window is a great idea, and hopefully more manufacturers take advantage of it, but until it becomes more mainstream, I don't think it's gonna happen. Plus, Multi-Window on Samsung would also have to then be compatible with other manufacturer's skins (LG, Moto, Sony, etc) and be coded the same way so that devs can actually do something with it.... it sucks, but I'm guessing this is the reason more apps are not compatible with it.
I'm willing to be told otherwise though. These are just my thoughts, with nothing other then an opinion to back it up...