Well, the best villains are those who believe in what they are doing. And I think, again, MOS would provide a very fitting rationale for what Brainiac is after. You know how Jor-El talks about Kryptons golden age of expansion and how the Krypton he knew had gradually declined? Or how Zod talks about Krypton having degenerate bloodlines that led Krypton to its state? Or how Jor-El tells Clark he can help Earth avoid Kryptons mistakes? Well what if Brainiac sees what he is doing capturing and immortalizing civilizations not as an aimless quest for knowledge but as a means of keeping civilizations from falling into decay? What if he believes he is actually immortalizing these worlds by taking the best of them and leaving the rest? Of course, tied into that could be a desire to resurrect his people or control all life in the universe or some other additional core goal, but I think at least as a primary goal, that could be interesting.