Data transfer from old iPhone to new iPhone

I’ll receive my new iPhone soon, so I’m now thinking of the best way to transfer my data from my old iPhone. May I know if using auto transfer will move the unwanted system data to my new phone as well? If so, would it be best that I simply set up my new phone from scratch? I also read that some people used auto transfer and the space of their photos doubled up in the new phone, so I’m worried. Thanks!