*spoiler* What was the point?

[Captain Squee]

I got all the cutscenes from the PP catalog, and there was one titled as, "secret" and so I watched it. It confused the crap outta me, can someone explain exactly what was going on? Why is cosmos alive? And what does she have to do with Lufenians? I was so lost

 

[The Illusive Man]

It's supposed to be a hint that the eternal war had not ended as Chaos and Cosmos has both planned and also hints at the possiblity of Dissidia 2 somewhere down the line.

 

[Neo Bahamut]

Honestly, while that is the usual interpretation, I really don't see it. The secret ending expresses quite a bit of finality. Cid even says that Cosmos is now the sole ruler of the world.

As for what she has to do with the Lufenians, it's time for my crazy theory. It's unverified, so take it with a grain of salt:

Cosmos & Chaos were created by the Lufenians. Chaos was created by accident from Garland, whom the Lufenians created as a weapon. Cosmos may or may not have evolved from the clone of Cid's wife. Cid was the driving force behind their ascension to godhood in either case, though.

Regardless of that, what we DO know is that Cid had been steering the conflict from behind the scenes, in an attempt to get revenge on the world for the death of his wife. He acted as a disembodied voice because he gave up his corporeal form in a deal with Shinryu, which led to the cycle of battle.