Not a bad hack. I've never read the manga, so the sentimental value might not be as strong for me, and some of the references might just fly over my head. That aside, however, I'm enjoying the unique twists Green's character brings to the traditional Pokemon games. Green always felt like an underdog compared to Red, Blue, and even Ash, and it's nice to see a prominent female main character in a Pokemon game once in a while.
That said, I do have a few nitpicks here and there.
Overall, this hack is probably the most satisfying one so far compared to the others I've played like AshGray or Expert Emerald, in the sense that it's bug/glitch-free (at least for now, up till the point where I'm playing at Mt. Moon), and it doesn't present any insurmountable difficulty spike, the latter of which is especially due to Green's lvl 100 Jiggly. Noting the latter point, however, that's where my nitpicking comes in. While I've not experienced the manga myself, I've browsed the Bulbapedia Wikia to do some research on the type of moves Green's Pokemon used, not to mention their nature and abilities... which quickly becomes a problem with the capture of Nidoran F, whom I discovered to possess the 'Rivalry' ability instead of the manga version's 'Poison Point' (as stated in the Wikia). Also, Jiggly doesn't know 'Sing', 'Tri-Attack,' or 'Disable.' I'm assuming that there might be a Move-Reminder later on in the game, seeing the large amount of Tiny/Big Mushrooms present, so Jiggly's issue isn't as big a problem as Nido's, and seeing that the Pokemon Encyclopedia's Save Editor doesn't work on hacked roms, I can't just change the abilities or moves as I see fit either, nor the gender for that matter (my Blasty's a female instead of the manga version's male).
In further updates, maybe you might consider fixing the gender, move-sets, and abilities such that these Pokemon start out having them by default when Green captured them. I love that I don't have to toss a Pokeball to capture Snubbull, which I'm guessing is due to an in-game scripted event. Maybe you could script something like that too for the ability/gender/move-sets as well. Just my opinion. :)
But like I said, the hack's pretty good so far, and I'm really enjoying it. Here's hoping for greater things to come.
Edit:
I take it back - just found out that Jigglypuff isn't suppose to be level 100 in your hack... Great. Now I'm going to have to start all over again or try to find a way to fix the glitch.