Do you have a version of this where you wrote your own code? When I think of hacks, I kind of think about the SMW game hacks that can be performed by Lunar Magic. I don't really know where it falls legally, maybe no worse than making a game based on someone else's characters, but I kind of have the impression that game companies frown upon it.
I get that a fan made pokemon game that is as playable as the original would probably not be liked by the likes of Nintendo anyway, unless maybe the creator of the game works for the company maybe, but I just have a few weird hangups associated with the word "hack" I guess.
I did play it, though, and technical legalities aside, it was a fun game. I didn't like how dark it got closer to the end, though. The player can actually choose to be a pretty good guy if he / she wants to, even buying pokeballs and catching and training their own pokemon, and I like that aspect of it, personally. I think people like Jessie and James because they aren't really bad guys; they steal stuff once in a while, but they never really cross the line, evidenced by the fact that their antics are tame enough for a kids' show.
Here are my suggestions:
I actually like catching and training pokemon in the game, so I did so when I could, even going so far as to purchase that useless Magicarp and raise it into a Gyrados during my hours of play. I think you should make stealing pokemon pretty difficult. It's a novelty that you actually can do so, but it also makes the game too easy. Maybe make the in-game repercussions for stealing pokemon, only pokemon, pretty harsh.
In the anime, Jessie and James are actually pokemon trainers. To me, they have more of a "lovable rogue" vibe. The police aren't constantly chasing them, and most of the dirty tricks they pull are to get back at Ash and company. They aren't straight-up gangsters. I think that's what makes them seem like characters you could have a bit of sympathy for. Now, there are other Team Rocket members in the anime who aren't like that at all. You want to see them lose, but I think it would be more interesting to let the player choose to be either a nasty evil criminal lowlife or sort of a "people's villain," who builds a reputation with the townsfolk of being trustworthy and occasionally doing bad deeds for good reasons, like Robin Hood or the Lone Ranger or something. In one or two episodes of the anime, Jessie and James were even mistaken for good guys.
You could start out having the player treated the same as any member of Team Rocket, totally shunned by regular citizens and only embraced by their organization, but you could have townsfolk gradually start to treat to a Team Rocket member who has proven himself/ herself a "people's villain" (like allowing the player an option to stop a team member, or criminal unaffiliated with Team Rocket, from mugging an innocent child or robbing a bank--hey, Team Rocket must keep up their image somehow. I doubt pokemon terrorists would be mistaken for superheroes, but Jessie and James are in at least one episode of the anime,) by giving them perks that they don't give other criminals. For instance, license to enter the gyms and battle, freedom to shop at pokemarts and go on training missions, their own starter pokemon, and the ability to walk around town without fear of being pounced on by self-righteous citizens who decide to take the law into their own hands. Tee-hee, you could even include a scene where Ash tries to mop the floor with your "people's villain" and the citizens come out, stop him, and beat him up with their pokemon!
On the other hand, you could treat players who decide to play nasty criminal lowlifes to being mobbed by self-righteous trainers (the team battles in the Pokemon Apollo game are nice, especially the one where the player is mobbed by a bunch of police with pokemon), banned from pokemarts and even pokemon centers, having their stolen pokemon confiscated, being attacked by wild pokemon who sense they are evil, etc.
Of course, every choice would have its own set of repercussions and rewards. The player who decided to be the evil villain could get rewarded by like-minded individuals on the team, like in this game, but the player who decided to be sort of a "good guy" and show himself/herself trustworthy to the townspeople could get rewarded and protected by those people. They could also get into regular scuffles with the evil criminal types, like Jessie and James sometimes do with Butch and Cassidy, as well as members of other criminal organizations, in the anime. Plus, there could always be the occasional misunderstanding, where the "good" bad guy gets the same awful treatment as the real criminals.
I just like the idea of the player being able to become sort of a Lone Ranger type character. You sort of gave us a good balance in the current game, but I kind of don't like that the player is rewarded nearly equally regardless of what choice he /she makes. The game could explore more themes if it were more responsive to the choices the player made.
Oh, and please give us more pokemon choices. It would be nice to be able to find better pokemon in the water and grass. Like I said earlier, I don't like that the player can just steal the pokemon he / she wants with nearly no repercussions. I feel like it makes the game too easy. Plus, I just like playing pokemon games like pokemon games, going on little quests, searching through the grass, battling trainers, finding cool items, wasting several hours, etc.
I would also like some fourth-wall breaking easter eggs, such as trainers with Game Sharks that will give you any pokemon you want if you are lucky enough to find them.