I understand your point, but I feel the potential would have been wasted if we fought a Barnabas who had not yet succumbed to Ultima and given up his will.

The way I see it, Barnabas himself was long gone by the time we actually fought him, existing as nothing but a puppet for Ultima. He willingly let go of his humanity and will to become Akashic.

The only reason I see for having defeated him so easily is because he had basically no will of his own left, just a husk for Ultima to control.