Awesome, I completed the main story, but I have no doubt there are still some secrets I can find in Aquaria. Starting by decrypting the texts and those 5 treasures that I am missing...
I must admit the first time I saw the ending (with the 3 memories), it was a lot of informations to take in at once and, thankfuly, I found this thread (and defeated the boss again to listen to the ending again after reading it!) to make most of the pieces of the puzzle connect with the others. It's a bit annoying when you are shown too much elements that you don't understand, we're all curious heh?

So there has been a lot of theories and ideas tossed around in this thread about how we should interpret the ending. Alec has kindly helped by giving a few hints to set us on the right direction and I guess it must have been fun for him and Derek to read what we understood of the story and the speculations for what might be following next! At this point I believe that the sunken city was the flying one, that the whole story we played was lived by Naija and that it is her son discovering her past from one of the blue crystal after she disappeared (see ending and introduction when you start a new game). Well, he discovers her past until the memories are "locked" by Mia.
It seems to me the girl we see at the end is the princess of Mithalas. Her skin is very similar to the prince and her ears match with that race. She has black hairs and seems to be wearing a diadem just like her portrait in her room. She also has a necklace very similar to the one Naija's son wears! But that might just be a coincidence.
Great game overall. I really enjoyed drifting in Eric/the creator's canvas!