Whether or not an ending bothers me simply depends on the story itself. I do tend to expect happy endings in safe, traditional games like Dragon Quest. I DO NOT expect it in more nuanced games, like Skyrim or Final Fantasy(FFX, for example, is actually bittersweet). Happy endings in grimdark would really be one hell of a subversion, imo, unless they are very much earned.
Given how Kellhus made is pretty damned clear that he wanted to possess, like every one, a happy ending in THE SECOND APOCALYPSE would most likely be a esoteric sort of happy ending. So, even if Kellhus DID succeed in stopping the Consult, unless something was done about Damnation, I can't help but think that not much would change beyond that, especially if he knows that those that he wants "saved" would be saved. The Ciphrang would be just another tool. Hell just another kingdom to rule. Every one would be equally enslaved, except poor Achamian, I bet.
I think TUC ending in general was pretty damned fitting and certainly NOT bittersweet, despite some survivors. "Downer ending" certainly fits and I LIKE IT(yea, for the wrong reasons, but still...)! An ideal ending just plain wouldn't happen and I know that. I do, however, agree that an Ajokli ending would have been appalling and would pretty much be the actual end.
As for TNG itself, I can't see it being anything other than bittersweet, with heavy emphasis on the bitter.