I've been playing this since last week (currently trying to solve one of the devious ice boulder puzzles

) , and it's safe to say I haven't had this much fun with an RPG Maker game for a LONG time. I can feel the love and effort you put into it. Your characters are written really well, the puzzles and minigames are surprisingly well-done for an RM game, and I LOVE that there's so many hidden treasures to find. You really reward player exploration, and that's something I don't see too often these days.
My only gripe up to now would be the over-use of Final Fantasy music. Admittedly, it's
good music, but some of the themes (like Aerith's Theme, for instance) are so iconic that they tend to break my immersion and remind me that I'm playing an RPG Maker game.
Apart from that, I'm having a blast. Manifest strikes me as a love letter to the classic SNES/PS1 RPGs of old, and is proof that it's possible make a lengthy, good-quality RM game without reinventing the wheel or adding umpteen bells and whistles.