An issue that fans took with the series was that several interesting villains were never used for more than three episodes at most before getting dropped for no apparent reason.
Blight was the biggest offender. He was the Big Bad of the first season and set up as the Big Bad of the series period...but nope, he never returned after the first season finale. The character did reappear in the comics, however — his body survived, but he doesn't seem to remember anything about his past life outside of hatred and a desire for vengeance for Batman and Paxton Powers and was eventually made into a target for the Stalker, and was eventually killed by being caught in a blast furnace.
Given the number of shippers rooting for her, Melanie may also count as this. For one of the most popular romantic pairings in the show, you'd think she'd appear in more than three episodes. She does appear again in the comics though.
Most of Terry's supporting cast was sorely underused, most prominently his mother Mary, followed by his brother Matt and his girlfriend Dana. For all that they tried to make Terry different from Bruce, they neglected the characters in Terry's life that Bruce could never have had.
Regarding Matt specifically, there are those who lament the missed opportunity of Matt's becoming a Robin Beyond to match Terry's Batman Beyond. It doesn't help fans' general ambivalence toward Matt.
Willie Watt, who's more of an example of, "They Wasted a Perfectly Good Superpower". Hints throughout his debut episode, especially the ending, implying that he's become a full Technopath who isn't just bonded to the Golem. This would've given him a host of advantages in Gotham's new cyberpunk setting, especially when facing off against Terry who relies a lot on his cybernetic costume. His second appearance ditches all of that and just gives him standard telekinesis.
Zander. Great Shadow Archetype, an interesting version of a Sheltered Aristocrat, then, well...he's turned into a dinosaur and killed off. The writers lament this one in the DVD audio commentary track, in nearly those exact words.
Victor Fries is one of the few members of Batman's original rogues gallery to come back, able to maintain a conversation with Terry (unlike, say, Bane), given new motivations (either revenge on Powers or atoning for his past), and given a new, enhanced suit. Then he commits suicide. His perspective on the new Gotham and the new Batman is never explored. This one isn’t as egregious, though, considering that “Meltdown” is generally considered one of the best, most tragic episodes in the DCAU.
A version of Talia al Ghul who is no longer under her father's thumb, is using his former empire to improve the world, and simply wants to reconnect with Bruce while offering him a chance to use the pit again, but with no real conflict. Sound good, right? Too bad that it's really just Ra's's soul in her body as part of an Evil Plan.
Given how the show tried to tie up loose ends about the most prominent supporting players in the original Batman's life, the absences of both Dick Grayson and Selina Kyle, coupled with the vague-at-best explanations for their respective fallings-out with Bruce, stand out as glaring.
Dr. Price, the military scientist who has a tenuous alliance with Batman in one episode, while being willing to acknowledge her own screw-up in making a weapon with an unstable reactor and putting herself in danger feels a bit like she could have been used in some of the later episodes dealing with the government.
