He ruled over a vast, complex array lands that match those of Charlemagne, the roman empire etc, but am I right in thinking he has been relatively neglected by historians given the amount of power he had (at least on paper)? What has driven this?
He receives plenty of attention from historians!
Here's the index entries for Charles V versus two vaguely contemporary kings from Thomas Brady's German Histories in the Age of Reformations, 1400-1650. That's a book that covers 250 years. Furthermore, Brady is not doing original research on Charles (at least, to my recollection)--he's hitting on that many topics just from previous scholars' work. AND this only covers one slice of the emperor's reign, religion/the Reformation.
The German Wiki page for Charles (Karl) V has a nice little bibliography section of books devoted to Charles, the emperor, rather than larger contemporary topics.
Is that helpful?