>>58067800Talking specifically about plot, there are so many different things that Team Rocket is invested in that are directly related to pokemon that taking the pokemon out of it makes them just... Random crime.
Stealing fossils on Mt. Moon? For reviving and selling pokemon, kinda makes sense if you replace it with extinct animals since that would still be crazy profitable. Recruiting people on Nugget Bridge? Unless you're literally just making a society that is REALLY into dog fighting then it doesn't make sense. Robbery in Cerulean is over a TM, which no longer exists unless the changes in the setting are so minor that its literally still just pokemon but called something different. Marowak and the Silph Scope, just normal poaching with an animal ghost. Still works as a story in and of itself, one of few things that translates well for a non pokemon story. Game Corner loses it's appeal as offering rare pokemon and TMs and just becomes an average casino. The takeover of Silph Co goes from being the take over of the company that makes pokeballs to being a 'just because' sort of thing. Giovanni secretly being a Gym Leader doesn't exist and wouldn't have the same gravitas in a non pokemon equivalent.
Funnily enough, Gen 2 TR's plot would fair better. All their actions translate well to a non pokemon setting. They are gangsters who are trying to regroup with a cult like loyalty to their boss. Slowpoke tails is simple poaching, Lake of Rage becomes make animals berserk to keep authorities busy, Radio Tower is all about contacting Giovanni with the potential to use the rage inducing radio signals being a secondary goal.