Can you explain what you mean by that, because in all honesty if were going by gen 1 obtaining pokemon and tailoring them to what you see fit isnt that much different from something like final fantasy were you get party members as you go, level them up and teach them stronger moves (hell the job system is almost like evolving your mons in a sense).
A typical RPG party will consist of distinct characters who have highly motivated personal reasons to get involved in the quest. Something related to their own personal circumstances, goals, grudges, etc.
Even something as early as Phantasy Star (1987) has decent characterization in this regard: each of the 4 playable characters has their own separate and well-established motivations for either starting or joining the quest, and most of them have direct ties to some of the boss encounters that you fight along the way. Alis starts the quest to avenge her brother's death. Myau joins in exchange for rescuing his master. Odin joins as repayment for being rescued and for the opportunity to slay Medusa. Lutz only really joins because you go to the trouble of getting a government summons to get him, but he still has something of a mini training arc in the battle with his mentor. Point is: the game is written in such a way as to give each of its playable characters motivation and reward along the journey.
Your party in Pokemon doesn't join you to fulfill their own goals. The player character catches them to fulfill theirs.
I think this partially stems from the implication that, in Gen 1 and 2's continuity, Pokemon are a relatively recent development in the history of Earth, not an established species in a fictional world altogether. They're less an established part of the world's ecosystem and moreso this bizarre phenomenon, with its research still in its infancy. Compare and contrast Professor Elm's reaction to seeing Mr. Pokemon's Togepi egg in Gens 2 and 4, and hearing that it hatched:
I always just took this as a poor reconciliation of new game mechanics with world-building. The idea of Pokemon eggs being a "new scientific discovery" came across as farcical on its face because it makes the Pokemon Professors look incredibly incompetent. It would've just made more sense to me if Gold/Silver treated them as a natural established fact of life and just ignored the question of "why weren't eggs in Red/Blue" altogether rather than try to make some weird justification about their sudden discovery.
I'll admit that the idea of
the Pokemon themselves as a relatively new scientific discovery is a pretty interesting way to square this, and something I never really gave much though to. Still, they can't be
too new to the continuity, seeing as how Oak and Agatha are implied to be rival Pokemon trainers from their youth.
EDIT: I want to touch upon this a little more:
I actually agree with this part vis-à-vis Gen 1 specifically, but mostly chalk it up to the series still trying to find its footing. "Pokemon actually are our friends and they love punching each other in the face" is established from the get-go, but at the same time, they're still treated as mysterious (pocket) monsters to be controlled and contained. Many trainers, who are not villainous in any terms, use whips, including Sabrina; you can gamble for Pokemon from the yakuza with no consequences (in fact, you have to do this if you want to complete the dex thanks to Porygon); throwing rocks at endangered species in the Safari Zone to provoke them is treated as a valid strategy in order to obtain them. There's a reason all of these aspects have been phased out as the series has progressed - it clashes really hard with the notion that these creatures are supposed to be friends.
There are a lot of reasons to read the original world of Pokemon Red & Blue as much less "utopian" than later entries portray it as. You touch upon many of them here.
Another big part of it for me is that Red & Blue are adjacent to Pulseman in my mind, which was the most recent work that Game Freak had released before Pokemon. There's a decent amount of overlapping themes between the two games, particularly when it comes to beings traveling in and out of cyberspace, and the whims of the mad scientists who utilize that tech.
In fact, it is the use of that technology itself that seems to have driven the villain of Pulseman mad with power in the first place. If you're familiar with the game (or even just heard of it) but haven't seen a proper breakdown of the intro dialogue between the villain and his creation, I think you should check it out because it's actually pretty cool:
Pulseman is the child born from this union, and the thrust of the game is that Pulseman ultimately has to kill his own father.
Even the computer interface featured in this scene is ripped straight out of The Fly:
Pretty heavy stuff.
