Photos missing when I upgraded to iphone6

These Apple documents may be of help:

Migrating from iPhoto for iOS to Photos on iOS 8 - Apple Support

Get help finding your Photos in iOS 8 or later - Apple Support

1 month ago I bought a new iPhone 6 and kept my old iphone5S (another phone no) same Apple ID and password, I backed up my old phone to ICloud as usual before I started up the new phone.

But did you restore your new iPhone using the backup of the old iPhone?

If you want the same photos on both iPhones, you need to copy the camera roll over, not just the photo stream in iCloud. The Photo Stream in iCloud only keeps the last month of photos. To copy the older photos from the Camera roll over to the new iPhone, including the older photos, restore the new iPhone using a backup from your old iPhone.

See this help document: iCloud: Backup and restore overview

Another option would be to upgrade to iCloud Photo Library (Beta) on both of your iPhones, if both can use iOS8. Then all your photos will be stored in iCloud, and both your iPhones will share the same Photos library, not only the last month of photos in the Photo Stream. This works well on iPhones, but not yet on a Mac.

See this link: iCloud: Backup and restore overview