I have done 3 playthroughs (the first one had to repeat it because I did not know about the possession feature xD) and I gotta say, one of the most entertaining roms that I have played, the story is very good and I am particularly interested on the rest of it and the trainer sprites are awesome nice art xD.
That being said there are a couple issues I see now that I have tried both Pokemon, first Abra its VERY underwhelming, its abilities are mid at best and the fact that it does not learn ANY move naturally makes it very bad, it is already a very big nerf that it cannot evolve but why make Abra so bad? if my feedback counts for something I would advice a rework of the Abra route with some of the following changes:
- Change abilities to things it will use ie instead of Mind Control only allowing Hypnosis to always land make it something like No Guard where all your skills hit regardless, or make it so you get a Dream Eater effect along with the guarantee Hypnosis so it is worth something, dunno if Purifying Salt description its incorrect or the Ghost protection means reduced damage from them but let me tell you that she still gets one shotted by Ghost moves so either look into that or change its effect to something like Magic Bounce which would be slightly more useful, Neuroforce its useless if Abra does not learn anything at all until you give it TMs but that is for another point, Magnet Pull seems like a very odd choice perhaps the most useless ability that Abra could have, she could benefit from something else like Prankster or something that covers its physical weakness like Fluffy or Fur Coat.
- Moves, while I can understand not giving Abra attacks that are too strong from the get go Psywave its a huge nerf, the unreliable damage, the low PP and the lack of actual super effective damage makes it so Abra cannot take advantage of its strengths at all, Confusion would have been way more balanced as a starting move and please allow it to learn more moves, it was hard enough to only have Psywave to use until I got TMs.
- Give Abra something that makes it worth taking her instead of Ghastly, the possession feature its very broken because each fight you have with a trainer you can choose which Pokemon you take with perfect IVs, maybe just a little luck with the nature and abilities but regardless if you choose correctly you get very good Pokemon besides the auto win to trainers who only have 1 Pokemon, you can get 2 Bulbasaur this way xD which in turn makes it better than getting 1 semi OP starter with Abra which you will get regardless down the line once you get Drowzee which again takes away from the uniqueness of using Abra, allow Abra to also take over someone in battle or auto catch a wild Pokemon or get discount or free items from vendors, things that will incentivize choosing her over Ghastly.
These are my main complains about the Abra route, all in all Ghastly gets you the better game experience xD, I know that the game is still in development and there are a lot of things that you may have already planned that just need time to implement but perhaps add more EV training items? a Macho Brace or give pokerus by default to your starter or something that makes the grind more bearable at least since money takes longer time to accumulate to purchase growth items. Also, I don't know if this was made on purpose but when you possess Team Rocket´s pokemon they don't get the perfect IV bonus from possession, though it was on purpose but figured I should mention it in case it was not intended, also with the possession ability that you inherit it would be better to either make it slightly random or allow you to choose which to inherit since a flying type with Levitate its redundant xD and having Bad Dreams on a pokemon that cannot put something to sleep its also kind of underwhelming, just mentioning it in case you were contemplating doing changes to that.
Thank you if you read all the way here xD and I will keep an eye on your project for future updates!