Just like the title says...my folder has 22K photos in it, which my iPad can handle size wise, but when I plug it in and sync it, it's only putting 13,300 of them on.
I just got a ipad mini and synced some photos..like you I wondered why they had not all synced but then I realised some of them were still in RAW and not edited and changed to JPG..maybe that is your problem too?