Well they weren't exactly rejected and I'm sure someday FFIII will be added to the PS Vita supported titles. But until then you can always get around it: Download to PS3, Don't install it, copy directly to PS Vita. Simple and easy way to get non-Vita supported PSP titles to work!
EDIT: Square Enix just confirmed it will be PS Vita Compatible!
http://na.square-enix.com/finalfanta...le_now_for_pspNow you can experience FINAL FANTASY III and take the experience portably through the PlayStation Portable (PSP) and PlayStation Vita (PSVita)! All your favorite FINAL FANTASY titles from the PlayStation era are available at the palm of your hand, a thrilling experience for any Sony user!