The thing is though when you look at other Team Leaders, Maxie/Archie, Cyrus, and Lysandre they all have Crobats to show they aren't necessarily bad people but rather extremists, which is jarring especially considering Cyrus and Lysandre's plans. In fact part of Silver's character growth is enhanced by the fact that he too has a Crobat when he started to care about his Pokemon.
Ghetis, Giovanni and the Team Leaders in Snagem and Cipher don't have such Pokemon which shows that they are assholes, Ghetsis especially. Giovanni might an exception since at the end he did redeem himself and has a sense of honor, but it doesn't change the fact that by large Team Rocket considers Pokemon to be tools, not friends. In fact this is best shown in the anime, as much as I hate to say that. Besides Jessie, James and Meowth everyone in Team Rocket are dicks to their Pokemon, Butch and Cassidy actually used a machine to make their Pokemon stronger by forcing them to get Angry.
There may be exceptions to the rule, such as half of Plasma, the Team Rocket Trio, game Giovanni at the end, and Wes but by large I don't think Snagem as a whole can be considered questinably good if they are okay with Shadow Pokemon.