Q: Sync of new iPhone 6s - does not sync all photos

Do you have enough storage on iCloud for all? Are you using iCloud Photo Library?

iCloud Photo Library FAQ - Apple Support

Elikel wrote:

All my photos are currently storen on iCloud - I have enough storage on iCloud and on the iPhone with 64GB. I have stored the photos on an external disk plus iCloud.

I don't understand. Are all your photos on iCloud like you said above or are they not all in iCloud like you said on your original post? What issue are you having now?

Elikel wrote:

Sorry - I am quite paranoid with my photos and have them stored both on an external separate disk

That is a very good idea. I do the same. 

Are you still having an issue you need help with or not?

Would be best if you provide as much detail as you can on the issue.

You said that all the photos are in iCloud? If you log on to iCloud.com do you see them there?

Are you using iCloud Photo Library?

How are you trying to sync?

You are welcome, glad it helped.