Many memorable villains like the Common Cold or Mega Mom and Destructo Dad were only the main antagonists for one episode. More jarring with the latter two that their son later became a villain and they were mostly relegated to brief cameos in episodes featuring other villains, with no interaction or acknowledgement of this fact.
Word of God even acknowledges that it's a shame Numbuh 60 didn't get much development.
Chad being a villain. Though he had a few episodes where he was the main villain, for the most part he was treated like just another teenager that the KND had to face. It was only in T.R.E.A.T.Y. (the final non-special episode) that any sort of interesting relationship between him and the KND, Numbuh 1 in particular, was explored.
Two KND traitor agents who seemed to be important Arc Villains never really reappear after their debut:
Numbuh 12 was never seen again after she betrayed the KND and joined the teenagers after realizing that since she was almost 13 and would be decommissioned soon otherwise. She could've become the Arch-Enemy of Numbuh 86 like Cree is to Numbuh 5 and Chad to Numbuh 1.
Numbuh 206 completely vanishes from the series after escaping from his encounter with 86 in F.U.G.I.T.I.V.E. Season 6 planned to have him involved in some degree, but that didn't pan out for some reason.
Sector Z had a memorable role in Operation: Z.E.R.O. but after their big reveal that they were the Delightful Children brainwashed all along, the plot point is never revisited nor given any closure.
"The Steve", the leader of the teenagers, only appeared in the second to last episode of the series.
Maurice, aka Numbuh 9. He was introduced as something of a Good Counterpart to Chad and introduced the major plot point to the series that some of the elite operatives continued to work as deep agents for the KND, even after turning 13. After his introduction episode though, he more or less gets Demoted to Extra. It doesn't help that the Teens Next Door as a whole drop off the face of the show altogether as if they never existed until Operation T.R.E.A.T.Y to (supposedly) explain Chad being The Mole at the last minute, making it look like an Ass Pull instead.
As amazing as Vin Moosk was in his only episode, some fans believe he could’ve been used at least once more. One of the very rare COMPETENT and GOOD adults? Alas, one appearance is all he got.
Several of Sector V's parents are criminally underused.
Mrs. Uno is revealed to have been the former KND operative Numbuh 999 and was implied to be a legend on the same level as her husband. Yet this fact is only revealed in the series finale, preventing us from learning more about what she was like as an operative or even letting her son appreciate the fact that he comes from a Heroic Lineage. She doesn't even have her name revealed.
Mrs. Beetles not only never had her name revealed, unlike her husband, but barely had a presence in any episode she's featured in.
Both of the elder Lincolns never get face reveals or even name reveals and the only real backstory either of them get is that Mr. Lincoln used to be a clown, but then that, most of the drama with the family comes from Abby and Cree's strained relationship, which the parents are completely oblivious to.
Though technically in five episodes, Henrietta Von Marzipan was for the vast majority of her screentime under a curse that changed her gender and, apparently, personality (for theworse). She only appears as her true self for about 30 seconds at the end of Operation: C.A.R.A.M.E.L.. Henrietta could've used at least one more appearance for us to better see what she was really like as a good friend to Numbuh 5.
President Jimmy and his secretary Anna were very memorable child antagonists and yet only appeared twice, with multiple questions left unanswered. For instance, we never learn if Jimmy was working for Father all along or even if he did so at the end of Operation: P.R.E.S.I.D.E.N.T. out of free will. It also would have been great to see an episode where Anna actually interacted onscreen with her uncle, the Common Cold (as mentioned above, he was an underutilized character in and of himself).
