The way I simply see it, is that Ulen Hibiki's Ultimate Coordinator and Aura Maha Cipher's Accord are two separate development branches of the Coordinator program.
- UC: solves the fertility and stillbirths issue plaguing the Coordinator race...which Fukuda seems to have forgotten about or glossed over. Also incorporates Newtype genes either because Ulen wanted the best of the best for his son or because he found those exotic genes stabilized the Coordinator genome.
- Accord: Coordinator with telepathic abilities, thus making them ideal to manipulate the masses and install themselves as leaders.
There is so far no evidence both programs were linked and shared notes, or that Ulen was competing with Aura to create the first Accord.
Also, there is no currently known evidence that the Accord technology solves the Coordinator fertility and pregnancy stability issues the UC program set out to resolve in the first place - which means they, too, could still be in a demographic/genetic pinch. Ulen's victory was short-lived given that Mendel was attacked by Blue Cosmos shortly after Caridad absconded with both Cagalli and Kira; much of the UC know-how probably died with the Hibikis and their assistants... Orphee being the same age as Kira, I don't think Aura had the time to refurbish his genome with UC material hypothetically pilfered from Mendel after the tragedy. I could be wrong, though - the novel hasn't been fully translated yet.
As for Kira, the novel (chapter 1) makes it clear Orphee views him as a "pest"...primarily because of his romantic entanglement with Lacus, though.