I know that Alduin is most likely the main antagonist in Skyrim, with the whole dragon thing going on, ect. But I'm pretty sure I read somewhere in Oblivion that Alduin was just the Nordic name for Akatosh. Seeing as how Akatosh played a big part in the end of Oblivion, it's unlikely that he comes back as evil. So is this an oversight by Bethesda or do I have my information wrong?

Well, Alduin is just the Nordic perspective of Akatosh, hes not really evil but they see him as the creator and destroyer of Nirn, who devours the world and leaves a new on in its place on regular intervals in his lifecylce, he is not the chief of the Nordic pantheon but its wellspring, albeit a grim and frightening one, also that since the Aedra were not made as good but a mix of good and evil, the Aedra as a whole may just be beginning to show thier side of evil... well really have to see just what dark secrets the gods hold for us ^_^

These Lore forum threads might shed some light (or dark) on the matter;

http://www.gamesas.com/index.php?/topic/1157744-akatoshalduin-in-skyrim
http://www.gamesas.com/index.php?/topic/1167116-the-nature-of-alduin