Warning: Spoilers of DOOM!
1. It's odd that each of the sentient races seemed to have been created by a god, except the Erulians. But I was just noticing that the energy temple god has an Erulian tail. Does that have something to do with the Krotite and their war against the Erulians?
2. We see Naija trapped in a blue crystal on the title screen and based on the secret ending we can assume that it was Mia who trapped her there. We see multiple blue crystals during the game, each of which has a spirit trapped inside it. Is that really Naija in the crystal, or just her spirit? It seems unlikely that it is actually Naija as Mia seemed to have plans for her and her powers.
3. Although Naija can live above water she doesn't seem to be particularly well adapted to it, in the game at least. Is Naija more mobile on land than we saw in game? Also do all her verse based abilities work above water?
4. At the end of the game it seems that each race was restored after the creator's death. Would they have been restored if their spirits hadn't been trapped in the blue crystals? Did Mia trap them in the crystals knowing they would be restored, or was she just providing Naija the power to defeat the creator and the restoration was an indirect result? Is Mia happy about the restoration of the sentient races of Aquaria, or angry, or does she even care? I didn't get the feeling that she planned on sticking around underwater for much longer...