But I think I've figured out what my problem is with the finale, and it's actually a problem with the entire direction of S5....
If you start a show and in the first episode you set up the premise that your hero is a warlock, he's living in a country that would execute him for being a warlock, and he's told that he needs to help the Prince of that country unite all the lands into one magnificent kingdom in which magic is restored and the Prince will accept the warlock as a true friend.... then well, THAT'S your quest. Your conclusion SHOULD be the success of that journey. Not something else.
I think the Merlin writers got caught up in the actual Arthurian legend and completely forgot what the point of the show they were actually writing was.
What S5 should have done was following Arthur and Merlin as they united the lands of Albion, following Arthur's journey as he slowly started to reconsider magic and whether it was truly evil (as he's done throughout the series, except for some reason in S5)... and then the magic reveal would be the climax, with the resolution being that Arthur accepts Merlin and Merlin becomes the adviser to Arthur in a Camelot lead Albion.
Because the only satisfying thing about the finale was the magic reveal, and watching Arthur work through the revelation until he came to accept and love Merlin as he truly was.
Meanwhile, the fact that a united Albion actually existed was a footnote, and we somehow missed its creation - it happened in the 3 years between S4 and S5, I guess. But that SHOULD have been a triumphant moment for Merlin, that SHOULD Have been the conclusion of his quest. We never did see magic being restored to the land - we could guess, that perhaps Gwen does it, but we don't even get confirmation on that. The truth of the matter is that the way S5 of Merlin was written, it was very much a tragedy...because while Merlin couldn't stop Arthur's death because it was "foretold", he somehow managed to completely fail at restoring magic to the land (that we saw) even though that was supposedly his destiny and very reason for being AND ALSO FORETOLD. So, Merlin failed to prevent the bad prophecies and yet the good prophecies never came true. Everything went completely wrong.
So, yeah, what I'm saying is that I'm disappointed. I mean, most of the episodes in S5 made for good viewing - and some of them WERE on the right track, but over all I'm disappointed.
We should have seen MORE of Arthur slowly coming to terms with magic, more of him questioning Merlin's odd behaviour and slowly coming to the realization that Merlin was more than he seemed... we should have seen more of Arthur creating Albion with Merlin's help, and then, when the reveal happened, we should have seen Arthur go through the same journey as he did in the actual finale, only the conclusion of the journey should have been him restoring magic to Camelot.
So, yeah, that's my two cents and the reason why I'm disappointed over all. The problem isn't the finale itself - the problem is that the writers equated the end of their show with the end of the actual Arthurian legend, completely forgetting that the premise and overarching quest in their show was DIFFERENT than Arthurian legend, and deserved a different end. Even if the Mordred's sword was still hanging over Arthur at the series finale, I think I would have been more satisfied with knowing that that was years down the road and Arthur and Merlin in the meantime had succeeded in creating Albion and restoring magic. I would have preferred to have left them in a good place rather than a place of grief and loneliness.