Okay I finished the game so I wanna give my thoughts since you asked.
I really liked the game but I do have my issues. It was difficult, real difficult. A lot more difficult than I wanted from a Pokemon game to the point it sometimes wasn't even fun to be honest. My final team ended up being Alakazam, Mega Rayquaza, Mega Charizard, Mega Starmie, Mega Tyranitar and Shadow Mewtwo. Not a pushover team at all, but I still struggled a lot especially near the end. I won't lie, because of this I abused the hell out of save states on Visual Boy Advance. Not proud of it but a lot of battles past the 8th gym, Altered Cave in particular, were annoying lol. I wanna go over some personal pros and cons for me just to help get my thoughts out.
Pros:
Starters. Based on what I saw playing the game, I'd rank them as Alakazam > Arbok > Machamp, but the beauty of it is all of them are great. It's not like Charizard Blastoise and Venusaur where one is clearly better than the other 2, and 1 is just plain bad. The fact that all 3 have the ability to set up too is just amazing lol. Personally think Machamp should've had the elemental punches (I assumed he would but he did not) to give his moveset more options but maybe that's just me.
EVs. Much, much better. Lowered the cost of vitamins significantly and made them the only way to raise EVs made it so EVs were optional and not annoying to deal with at all. Plus the fact many Pokemon (like Alakazam and Tyranitar) have a stat that's clearly much worse than the other 5 makes it very easy to decide which stat is getting ignored.
Pokemon Changes. There's SOOOOOO many good Pokemon options you can use if you want to. I changed my team so many times just because I could. Also having the choice to get Shadow Mewtwo + Rayquaza after the Champion to ease up the difficulty a little was very much appreciated.
Moves Changes/HMs. Mostly making moves more viable, I didn't see a single change in a move I didn't like throughout the entire game. HMs being removable is a godsend, having the ability to use and remove any HM as needed is something I always wished mainline games did.
Documents. Not really an in-game pro but something I loved nonetheless. Adding the txt documents with the game was really really nice, I looked through them CONSTANTLY while I was playing and I can't even exaggerate how big of a help they were.
Niches. They're cool but require getting used to especially when you know a lot of gen 3 by heart. It would really catch me off guard to not be able to hit Dark types with Dragon type moves for example lol. Same with a lot of typings.
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Cons:
Disobeying Pokemon. I don't like or understand this at all. I like being able to grind until I'm satisfied with where I'm at. To me it's half the fun, I would want to train up because I was having a hard time and wanted to get ahead but then I'd remember if I trained too much I would be penalized. Because of this I avoided fighting the generation trainers placed in gym battle cities. Why punish people for having fun and grinding? Felt forced to stay under leveled until beating the 8th gym.
No Items During Battles. I also don't like or understand this at all either. The game's difficult enough with or without this, but at least give people the choice. Why force a handicap that's unnecessary for the sake of upgrading something from difficult to annoyingly difficult?
*Just to note, the questions asked were meant to be towards myself and rhetorical. I know you have your own reasons that you already mentioned for including the features you did in your game so please don't take it personally :)
Altered Cave. Not actually a con, just didn't know where else to put this in this post. I really wanted to be able to get the unique Pokemon they had there lol. Like either in the cave itself or as a reward for beating them would've been really cool. The Pokemon themselves being included was really cool.
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That was a lot more than I thought it'd be lol. So yeah, all in all I enjoyed the game a lot and I'm definitely looking forward to the sequel when it's complete, whenever that'll be. :D