I don't think Meowth or Togepi are even close to evil. Togepi was just misheivous, like Jigglypuff drawing on your face when you fall asleep or Clefairy stealing your belongings. They are all fairy pokemon afterall, and in folklore fairies are pranksters who hide your keys, enchant you to dance with them, and switch babies with changelings.
Meowth is a survivior, not evil. The reason he got into the criminal life was because he was on the street with nothing to eat. He was pretty much your average stray cat picking through the garbages for bones. There was nobody to take care of him, and the people he happened to encounter were bullies that would tie him up and hang him from trees, and abuse him. Theren't weren't any alternatives for Meowth.
The Squirtle Squad seemed to take more enjoyment out of the risk of criminal activity than Meowth necessarily did initially. With Meowth it was more like, 'okay, this is how I can stay alive.' The squirtles certainly weren't evil either. They were just abandoned pokemon who vandalized things and kidnapped people because they wanted someone to pay attention to them.
Meowth is just as capable as the next pokemon of forming attachments to people and other pokemon. I think that is more of the reason he stays with Team Rocket. It is a job, but also Jesse and James are the closest things he has to trainers or friends. He has even displayed a twinge of empathy before for Ash, Pikachu and their companions in certain situations. He is a well-developed character who throws in on the side of good every once in awhile.
It is hard to find an example of an evil pokemon in the anime. Some of the dex entries in-game and mystery dungeon plotlines may go in a different direction, but as far as the movies and tv shows go it is people who are in the wrong 99.9% of the time, and not the pokemon. It is a reoccurring theme for people to see an intimidating-looking pokemon and immediately blame them for everything, only to have their first impression proven wrong, realizing that the pokemon they pre-judged as dangerous was really the good guy trying to warn and help them like Absol, Darkrai and Dusknoir.
Even pokemon that engage in really destructive behavior have been supplied with no shortage of reasons for doing so in the anime canon. Often it's reactionary behavior like the Tentacool and Tentacruel who attacked the city because they were losing their habbitats, or Mewtwo refusing to be exploited by humans and wanting to change the system.
At other times pokemon are just under command of trainers, and shouldn't be held to a moral responsibility for their trainer's wishes any more than a security dog following their master's instructions. If a master orders the dog to attack an innocent person and it obeys then that fault lies solely with the human being. Some situations feature eve m9re extreme physical or psychological coercion at the hands of humans like zoroark causing illusions under threat that her baby will be hurt if she doesn't comply in the 13th movie, or Celebi being possesed by by the dark ball in the 4th movie.
The one-off where a pokemon just seems to love power and hypnotize people for fun is the brief malamar plotline in XY, but again this is such an anamoly, and seeing as other good Malamar and Inkay are introduced too I don't even know if I should count this or not.
