FAT32 will work fine, although you can use other file systems if your ROM/kernel supports them, such as ext4, which includes journaling.
NTFS and FAT32 are rather poor file systems to use anyway, but it the decision was made to go with FAT32 for the sake of versatility: Windoze is incompatible with everything else and most microSD cards come with this format. The real question to be asking is when Microsoft is going to support other file system formats, as its competitors have for years.