Looking at the list of Astra type moves, I'm a bit concerned about Atmos Blaze. Granted, I'm not sure how high of a level you plan to make the opponents that wield those moves, their stats, etc., but having a 90 power +3 (!) priority move that can't miss and is guaranteed to be super effective sounds a bit broken. Especially if it gets STAB... *shudders* However, like I said, depending on the levels and stats of the things that use these moves, it may get balanced out in the end. As you said, they're reserved for superbosses, but still, I'm guessing a 180/360 power move (or 260/520 with STAB) off even a decent special attack stat would do major damage, if not completely OHKO a puppet (especially if you're using a dual type, since they'll take 4X damage), before they can even get an attack off. That's really the only move I have a problem with, though (although Cosmic Laser is also a wee bit concerning, although not as much as Atmos Blaze, IMO). Otherwise, I like the idea of superbosses having a type like Astra. A question about Alignment, though: are accuracy and evasion increased as well (yes, I know it says "all stats," but accuracy and evasion are a bit weird as stats, IMO)?
Anyway, I've played a bit of the game, and some things I'd like to note/ask:
The sound effect when booting up and closing the PC is way louder than anything else.
This is probably just me being a dummy, but in regards to the screenshot feature, the game says that they're saved in the same folder the game save data is kept. However, I'm not sure where the game save data is kept (and thus, I don't know where my screenshots are kept). Speaking of not being able to find things, you made mention of a readme in the OP, but unless I'm missing something, it doesn't appear as if one exists.
In regards to difficulty, the game's been laughably easy so far, honestly. Granted, I've only just beaten the first rival battle, but I picked Chibi Reisen, and she starts out with a Reason move, Confusion, meaning I have a move that's super effective against Silver's Chibi Sanae. I was also at level 10 when I fought him, and nearly OHKOed him thanks to the 4 level advantage I had, in addition to the super effective move.
Finally, this isn't really related to the game, but the "Personal Webpage" link in the OP links to some site offering tips to protect against phishing, as opposed to a site about this project.
I've also noticed some instances where text gets... cut off, I guess, but I'll wait to post those until I hear about the screenshot thing, since I took screens of all of them.
Overall, though, based on the little bit of it that I've played, it could be interesting as long as the difficulty/level curve increases.