Eustace Strych was terrible in Billion Dollar Boy but I found him alright in King of Mars and League of Villains. I actually don't remember the JTPH3 appearance much as it was very brief.
One of my least favorite characters is Judy, Jimmy's mom - not herself, but rather the way the writers used her. She had a lot of potential as in the movie and some early episodes like See Jimmy Run they made it clear that she was where Jimmy got his genius IQ from, but in general throughout the series she just functioned as a stereotypical sitcom mother/housewife. Because she's clearly very talented, I think she should've gotten more badass moments like Cindy did later on. This would've made her a better character IMO.
I also hate Nick (partially because Cindy's crush on him feels unnatural) and April and Betty Quilan, again because I don't like their ships (Um? Hello? Jimmy? There's a little someone I'd like you to meet called CINDY! YOUR ONLY REAL CRUSH!)