First of all, Hylia?
If you were a professional game development company you'd have a lawsuit happen here for copying tLoz with Hyrule/Hylia.
Second, I don't like it when people use 'Modern' Pokémon buildings in PMD fan games, it ruins the whole perspective of it being a non human world. Try to find some PMd tiles to use, or get some custom ones. Just not the Main series tiles.
Thirdly, Power? I don't understand why you've used the term 'Power'. Time & Darkness were used because you explore Time & and Darkness, as with sky, how does one explore power, exactly?
Finally, the main plot seems too much like a Pokémon Main Series game. Collecting badges and stuff, if this were to be a PMD, it should at least follow the usual, world in danger, strange pokémon, once a human, kinda thing.
That's all, I wish you luck with this!