Bonnie reminds me of a female Pokemon trainer. She has cut-off shorts like
the female trainer from Black and White 1, and black leggings like
the female trainer from Black and White 2. I feel like a Pokeball wouldn't look out of place in her hand. This isn't criticism or anything, just an observation...anyway!
I like Bonnie's overall design and color scheme. When I first saw her, though, I wondered for a moment if she was a man in drag. Something about the facial structure on the first picture makes her look mannish - might be the thick eyebrows and no feminine lips. But the second picture of her makes her look much, much more feminine. I also kinda feel like her arms a bit muscular for a female character...I know you're aiming for a "tomboy" character, but I feel like she's almost starting to border "butch" in that picture on the left.
Still, though, the first things that came to mind were "Serious and unfeminine woman". Somebody once said that the key to good character design is "The viewer should know exactly what type of person your character is, after just one glance." so I guess you succeeded, as far as that goes! However, that second picture of Bonnie made me think "Sexy gunmoll bimbo". I guess there perfect balance might be somewhere in-between those two pictures.
Nothing about her says "vigilante" to me, though. If I'd had to guess at her profession, I might have eventually arrived at "bounty hunter", but it wouldn't have been my first guess. At the same time, I don't really know what I'd change about her to make her more vigilante-esque. Utility belt or something? What weapons does she use? Where does she holster her gun?
As for Clyde, I don't have much to say. I don't think "mysterious" so much as "shady and sneaky". I hate overcomplicated character design, but "shady guy in trenchcoat and fedora hiding his eyes" doesn't really make this character feel too memorable to me. If I didn't know he was one of the two main characters, I'd say he was a henchmen's mook who isn't seen after episode 1.
Of course, I don't actually have a formal education in character design, and nobody ever seems to like the characters that I design, so maybe everything I said above should be completely disregarded!