DSi to 3DS tansfers: Saves not allowed

[alfredofroylan]

So yes you can transer everything, except saves, mostly to prevent exploits from past hacks:

Your DSi Ware save data and DSi Points cannot be transferred over. Save data will be deleted from the original DSi/XL system along with the DSi Ware game.

http://www.andriasang.com/e/blog/2011/06/02/3ds_software_transfers/