I'm not sure what the story is about the voice actors. The problem is that the Timmverse shows have usually been excellent at finding THE perfect actor for the particular role. Even the roles of supporting characters or villians; heck, they had to do that for Superman TWICE (and at this point, I like Newburn just as much as I liked Daly on the S:TAS series; Newburn's voiced Superman for more episodes overall). Clancy Brown especially proved that he IS Lex Luthor in this last JLU season, which focused heavilly on Luthor. From being cerebral to being angry to being obsessed and even enraged, Luthor had a wide range of emotions this season and Clancy did it all. Burton's also the only Brainiac for me. I'm not sure why they weren't available; maybe they were too busy on JLU and other shows, and it seems obvious that BRAINIAC ATTACKS was quickly decided upon, funded, with a strict deadline. DC wanted this animated movie out around when SUPERMAN RETURNS hit the big screens, and if that meant skimping on some of the villians, I guess that was a worthy sacrifice (especially after getting Tim Daly to return to the role; after all, he skipped on JUSTICE LEAGUE). The voicework is done before any animation is done, so with the deadline strict, they maybe didn't have enough time to wait maybe a few extra days/weeks for Burton or Brown. Both are busy VA's, especially Burton.
Given how JLU has ended, I doubt this story will fit very well into the "Timmverse" much, unless you count it as after S:TAS's finale with "Legacy", but before JUSTICE LEAGUE. Say what you will about MYSTERY OF THE BATWOMAN, but at least Timm had more of a hand in that, and it fit into JL's continuity perfectly.