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I don't know if I'm blowing this out of proportion, but I absolutely loathe how you're unable to get more than one mon in Super, unless it's a mon with a gender difference that Spike Chunsoft didn't forget. Breaks get a lot of justified flak, but I feel like this gets overlooked for some reason, with people only focusing on "I hate how you recruit mons" instead of "I hate the limitations behind it." There's plenty of movesets that are exclusive to certain mons, and in Sky, you had more than enough room to get duplicates even after getting all 492 Pokemon. This allowed you to get a second or even third mon to use, so you can give them an alternate moveset so they can fulfill a separate role without having to butcher or reset the mon you currently had. With Pokemon now only having one ability (I know Gates introduced this first, but Super kept it) it'd be perfect to have two same species mons with different abilities, since that would change their function completely.
>just use their pre-evos
Some Pokemon can only learn certain moves once they evolve, like Vileplume being the only one with access to Aromatherapy. Plenty of Pokemon also change abilities too, like Slakoth to Vigoroth, or types, like Azurill to Marill.
>evolve them
Remember, only one of any species. If I do that, they're gone for good now.
>use a different Pokemon entirely
Some Pokemon have multiple unique movesets. The most obvious one is Smeargle, who has access to almost any combination of moves. No other Pokemon can substitute for that.
>can't you just relearn all those moves, or change abilities?
Tutor moves are pricy, and changing abilities also costs a gold bar. This adds up fast if a certain mon plays a significant role in many of your teams. Also, going back to Smeargle, relearning an entire moveset every time you wanted to run something different would be a pain in the butt.
It's a shame too, after Sky and Gates managed to refine the recruiting system to such a significant degree.