I just got a 3DS XL system and I want to move my 3DS profile to the new handheld. Will the System Transfer also transfer my StreetPass progress? I've finished several panels and received several Find Mii hats, I would hate to lose this progress just because I got a new system.
I went ahead and did the System Transfer (can be found under Settings -> Other Settings -> System Transfer (3rd page, I believe). My StreetPass data and progress was transferred although data that was stored on SD card (such as some DLC and extra data for some games) was lost.
No. Everything from your old 3DS will be moved to your new 3DS. After the transfer is complete, make sure you swap sD cards. (Put your old SD to your new 3DS)