I think WMV should stay on the windows platform and the 360 as well as Quicktime. I want MPEG on the PS3 in every shade that has been made and will be made, be it MPHOLO1 or MPEG1. Windows media and Quicktime is bastard formats created by Companies to keep lock on their users to their platform.
To my surprise my collection of Music videos turned out to be primarily MPEG so i´m happy. The fight right now is getting the few .AVI files turned into MP4 in the most quality sustaining and space saving way
I will turn my PS3 into the Center for my media stuff and thanks to AAC/MP4/MPEG2 the stuff can be played cross platform as well.
In regards to filesizes, i think one of the problems might be license cost, and since Microsofts monopoly on the PC requires whatever devices you may use on the PS3 to be supported as well, FAT32 may have been the cheapest way.
NTFS may be considered a server technology with the license cost* to follow.
*
http://www.ft.com/cms/s/cea4b0c4-e2e3-11db-a1c9-000b5df10621.html
AFAIK MP4 and MOV are the same thing (containers for a given codec). WMV is a contaner as well. The codecs that we all shoud care about are VC-1 (used by pretty much all HD-DVD's and all MS Marketplace video media downloads). And H.264 (Used by most Blueray movies and used by all modern QT video files)
Quicktime
MP4 is based on Quicktime
WMV
VC-1 is based on WMV