Before reading this, understand that a lot of this is pretty subjective.
First of all, we know that Meta Knight is a good guy for the most part with the exception of a few games. He was a threat and we never knew why.
Second of all, the Kirby anime, even though it wasn't canon, showed us that the Nightmare wizard created Kirby.
Third, the anime showed us Nightmare could possess people.
Meta Knight unmasked is the same species as Kirby, so it could be assumed that he was also created by Nightmare. Just as Kirby was one of his mistakes, as said in the show, I think Meta Knight and Galacta Knight were mistakes as well. Meta Knight avoided telling people this information for anyone who knew about Kirby's creator. That's why he wears a mask; to hide his identity so he's not judged as being a monster. Along the line, it is my theory that Meta Knight was possessed. In the two games in which he is a threat, Kirby's Adventure/Nightmare in Dream Land and Kirby Superstar/Superstar Ultra, there is a mode called Meta Knightmare; almost implying that Nightmare is somehow responsible. There is also a song tune in Super Star called The Nightmare Warship, again implying that Nightmare is somehow connected. When Galacta Knight found out about Meta Knight's possession, he assumed the same for Kirby, which is why they fought. Because of Return to Dream Land, and because of Magolor's dialog indicating that this is now time after, Meta Knight must have been recovered some how, but Galacta Knight still thinks the same of them.
One thing that you'll notice wrong about this theory is that Nova said he sealed Galacta Knight away a long time ago. Could it be that he did that for the Star Warrior's protection, assuming Galacta Knight is also a star warrior, perhaps the leader. The show mentioned that there have been many Star Warriors lost, so only a few still exist. The angel wings on Galacta Knight could be symbolic for the highest form of good, and the bat wings on Meta Knight could be symbolic for evil.
What do you think?