After waiting a long time, sky3ds team release the new firmware finally. Please see the below:
Sky3DS+ firmware V130 [02/13/2017]
1.The new AP check issue fixed.
2.exFAT support added.
3. Upgrade from FAT32 SD ONLY!(this will always be FAT32)
How to use sky3ds+ to play Pokemon Sun/Moon?
Step 1. Connect PC, update your sky3ds+ to the latest V130 firmware
Step 2. Download the rom of Pokemon Sun/Moon from reliable sources, make sure it’s no modified and edited. Then copy it directly to the FAT32 microSD card. As the new firmware V130 supports exFat, it means you can put rom over 4GB to your microSD card and there is no need to trim.
Step 3. Innsert the microSD card to sky3ds+, then insert it to your 3DS console.
Step 4. Power on, the game icon will appear on the screen, press A to start the game.