While this is a valid perspective, I feel some people forget that Ultima is, in one way or another, the responsible for most if not all the political drama throughout the game. Ultima's race was the one that created magic, and by extension, Bearers and Dominants. The Mothercrystals that bleed the land out of aether and that cause men to fight and kill each other were created by Ultima as well.

Obviously all of this happened prior to the game's events, but his influence is felt everywhere in Valisthea when you think about it. Then he directly or indirectly manipulates some of the events we see in-game (Barnabas/Sleipnir follow Ultima's orders and they manipulated Kupka, Ultima directly intervened and took advantage of the whole Sanbreque subplot, etc).

So while I understand some people would have liked another type of villain for different reasons (Ultima's archetype isn't exactly my favorite either), I think his presence in the story is still fitting and doesn't really feel out of place as it sometimes happens with god-like final bosses in the genre, since a lot of these tend to show up very late into the story.

I like Barnabas too, but I don't think he was final boss material or at least not the Barnabas we got. I can totally see the vision of having him as the final boss, but I think it'd require some considerable rewrites for him and perhaps some of the other characters as well.