First of all, I'd like to say that I like the core mechanics behind this hack. A) It's harder. B) You can catch any pokemon, excluding the few you mentioned. C) No trade level-ups. Thank god. This is the sort of hack I can really enjoy--especially since it's one of Crystal.
But my praise comes not without criticisms. I'm noticing a lot of minor things that gives the game a sort of 'unpolished' or 'rushed' feel. For instance, the starters are Charmander, Squirtle, and Bulbasaur, yet the text and speech read the Johto starters. In some areas, such as Rock Tunnel after the Ruins of Alph puzzle, I exit only to find myself in Viridian City. When I enter a building, it informs me I am in Cianwood or Azalea town. These errors are small, but they add up.
I'm not seeing any major issues, honestly, besides text-based ones. Good work on the hack.