I personally would wager that most of those weren't really intended as "send off" episodes, but rather just more stories with those particular villains. They just seem more final than they are because they were the last ones for those characters in that particular run of episodes.
Ehh, from what I understand,
Zeta Project implies 40 years, while
Batman Beyond more consistently implies 50. But all shows have these sorts of inconsistencies/growing pains. And it helps to remember that TZP wasn't from the same team of people as BB.
It helps to cast someone who can drive themselves into the studio for a voice recording!

Tim Matheson was driving himself to the studio when he was playing the 10-year-old Jonny Quest in 1964, so he was obviously older than his character.
Yeah, I still don't really know where to put the Jason Todd stuff into my timeline, and I'm not entirely sure if I want to.
Yeah, probably. Maybe we should spin the timeline discussion off into its own thread?
On the topic of Kevin Conroy's possible "replacement" as Batman, I don't think we're going to see one person play the part to the degree he did for a long, long time. It's probably just going to be a bunch of different actors playing the part for a project or two. When Mel Blanc passed away, there wasn't any ONE person who took over all of his voices, because: A) No one else was that versatile, and B) Different directors had different preferences for their projects. One director might prefer Actor A as Daffy Duck, while another prefers Actor B's Daffy.