Well, if you consider Thomas from a female character's perspective, he's just being nice, and he really does want to see someone succeed where he failed. The poor guy has been living in shame since he lost his family (both family members were female), mainly because of his inaction, and he's probably trying to atone for his past behavior (much like Yuria), although he still doubts himself.
As for Mephistopheles, she's just evil and arrogant (the name alone tells you her story). Her deep, echoing voice probably has more to do with demonic possession than anything else. After all, her not-so-secret society specializes in the soul arts. The shoulder pads on the Rogue's clothes are what make her shoulders appear to be so broad, so her physical build isn't different from the typical female characters.
If anyone creeps me out, it's Saint Urbain's female follower. She's practically in heat over Urbain. lol
