I don't know if this is a popular theory but the idea that the prophecy did not come true because Merlin was no longer Merlin by the end, so he couldn't save Arthur.
Killgarah tells us in s1 that in order to unite Albion, Arthur and MERLIN have to work together. However, as Merlin slowly stops working WITH Arthur and instead starts working FOR Arthur he chips away the pieces that were Merlin. Gaius even implies that when he asks Merlin about the boy who walked in his chambers years ago.
The Merlin who would've united Albion would've helped Morgana, wouldn't have isolated Mordred, wouldn't have lied to Arthur about his thoughts, wouldn't have hidden Morgana's involvement with GwenCelot. All of these things pushed the idea of Albion further away, because all of these things pushed Merlin away from being Merlin. In a way, he got so concerned with being Emrys, that he forgot that Emrys was just a name for Merlin and not two different identities.
It's like how in a Greek Tragedy the main character tried his best to stop the passage of the prophecy, therefore actually making it happen. Merlin did the opposite, where he tried his best to make the prophecy come true therefore accidentally ended up sabotaging it.
I think this also plays into Arthur coming back from Lake Avalon. Arthur fulfilled his end of the deal: He became a just, noble ruler, and therefore he was rewarded with eternal rest with his wife, and his knights. Merlin on the other hand deviated from his nature, and did not remain true to himself, and is therefore cursed with eternal exhaustion and isolation in the real world.
