I’m not sure whether I’ve discussed it yet or not either. It sounds like the sort of thing I might talk about. Could have come up in passing.
I think the obvious answer is that, in keeping with the franchise’s normal stance on what it takes to be a good trainer, most of the grunts for the various evil Teams are just not very nice people. The more happy and fulfilled your Pokémon are, the more dedicated, energetic and creative they can be. Most members of Team Aqua, Team Magma and Team Galactic are little more than thugs and may not be giving them the kind of emotional stimulation they need; Team Rocket certainly don’t. Some members of Team Plasma are genuinely decent people, but most of them are also avowedly distant from their Pokémon because they intend to release them and don’t want to get attached. Team Flare may have a similar rationale, if they’re aware that Lysandre’s plan for a new world involves the extermination of Pokémon as well as other humans.
Actually, I think the more interesting question is why the Pokémon belonging to the leaders of these groups are not shite. In many cases it probably has something to do with the genuine charisma of these figures – Giovanni, Maxie, Archie, Cyrus, Ghetsis and Lysandre all have very strong personalities and a great capacity to lead (on top of which, Maxie, Archie and especially Lysandre have legitimately noble personality traits as well – although one must wonder whether Lysandre’s Pokémon know the full extent of what he has in mind). Their Pokémon may admire them every bit as much as their human followers, to the extent that they can ignore any deficiencies in the affection they receive – and might, through that admiration, come to emulate their trainers’ moral and ethical leanings, in much the same way as Pikachu emulates Ash’s…
Pokémaniacal 