...ad hominem?
Really?
How intelligent you make your pokemon definitely depends on the needs of your particular story, just like you have all kinds of fiction showing real-world animals at all different levels of intelligence. There are stories that attempt to show animals at an actual animal-level intelligence all the way up to Redwall-style narratives where they build abbeys and wield swords and whatnot. Even within just the journeyfic genre, you can get different effects by choosing different places on the spectrum. For example, a story that's going to be more about the human character(s) and their relationships might benefit from using more animalistic pokemon, simply because it removes some of the weirdness of the pokemon rarely being seen outside of being used to battle and/or not appearing to think for themselves, which happens in an uncomfortable number of stories where the pokemon are clearly supposed to be intelligent agents (see in particular many Nuzlocke fics).
For my preference, I like to use pokemon that have a similar level of intelligence to humans, but not necessarily the same kind; they have different goals and priorities and perceive the world differently than humans do. I don't think I succeed particularly well at that, but that's what I aim for at least. I imagine that different species of pokemon might have different levels of intelligence, based on their wildly different biologies, as well. I think the idea that pokemon actually increase in intelligence as a result of being around humans is an interesting one and could be cool to use in a 'fic, but I don't think I've really seen anybody playing with it before, although I've seen it suggested several times. However...
...and also we know that life as a trained mon is better than living in the wild, having to worry every night if you'll survive to see the day, whereas under a legalized battle the worst risk is that of falling unconscious and waking up next to a hot Chansey.
IIII don't think we know that at all, actually. If pokemon form their own societies out in the wild, then they presumably have some form of social structure that serves to support them. There's no indication that living in the wild is necessarily a grim day-to-day struggle just to survive, any more than living in human society is a grim day-to-day struggle just to survive.
Not to mention that the games and anime have numerous,
numerous plotlines that show the various ways that humans abuse their power over pokemon. Maybe a pokemon would prefer to hang out with a human who was going to treat it well, but to say that having a trainer is
inherently more desirable than living in the wild seems a bit of a stretch. Not all trainers are good; the worst that could happen after losing an officially sanctioned battle is waking up with your heart closed and the complete inability to feel normal emotions, or have your trainer inflict some form of punishment on you, or abandon you in a completely unfamiliar environment, or in a Nuzlocke story, actual death. And even if we were to say that all trainers are good trainers, it seems reasonable that some fraction of pokemon consider giving up (some of) their freedom too high a price for whatever luxuries might come with being trained.
I don't think there's any problem with saying that pokemon want to be trained, in general; it's just that I don't see it as necessarily erasing some of the ethical issues that surround pokemon training if you look at it using real-world reasoning. Like, okay, so pokemon benefit from being with humans. But should partaking of that benefit require them to submit to capture? (And if you don't want to try to apply real-world reasoning to pokemon training in your story, that's fine, too; the issue is more with stories that try to do this but fail.)
As for what makes a better story, my impression is that having Pokémon that can at least want things for themselves, regardless of how much intelligence is needed for that, is one of the main driving points for a good story featuring Pokémon.
This is certainly true, though. Most good characters require motivations that will drive them to act throughout the story, so one way or another, if you want the pokemon to be major players in your story, you'll need them to have at least some degree of both desire and agency. The level and kind of intelligence used just influences what those desires are likely to be and how the pokemon acts to satisfy them.