For an htpc I would recommend using your favorite linux distro and installing xbmc standalone on top of that as it often comes packed with a lot more stuff you often actually need and its easier to change things that the very much stripped down xbmcbuntu I have not really seen a performance difference between the two options and the storage usage is still very low, I would say that installing it ontop of another distro is better than using xbmcbuntu.
I would recommend it over windows because of the startup time and resource usage, a htpc running on linux will generally do perfectly fine with just 1gb of ram while one running on windows would clearly be better off with 2gb, as for the startup time windows just starts up a lot slower. In addition to that a legal copy of windows is far to expensive to waste on a htpc unless you want it a bit beefier and do some gaming on it. If you are going to use windows, mediaportal is also a great mediacenter as you can tweak and change it a lot more and the scrapers for it are a lot better than the xbmc scrapers mainly because they are dedicated addons and not part of mediaportal itself. as for plex I never really tried it.