How can I transfer annotations from a PDF to another in iPad?
GoodReader can't do this and GoodReader suppport is unaware of a product that can, since they operate in this space I assume there isn't an iOS app for this.

GoodReader can display PDF files, add annotations to them, and save those annotations to that specific file. Unfortunately it's not able to edit the content of a PDF file, merge files or create new PDF files.

On a computer, the software that does this is Adobe Acrobat Pro. Unfortunately I can't recommend an iOS app that can perform these functions.