Chiming in here from the SEO team at Wikia with a couple of thoughts.
Some context: Googlebot and other search bots seek to mimic human behavior in evaluating content, so modern SEO is all about user experience. Old school keyword and link manipulation is out of date; search algorithms are too sophisticated and organic search rankings are too closely tied to user behavior. In truth, both users and search bots prefer accurate page titles and site architecture that aids content discovery.
From the proposed options, I prefer the naming convention Mrkermit outlined (most well-known name, omit Earth-616, including the real name in parenthesis optional) for both UX and SEO reasons.
Page headings and titles are strong, strong signals, so the best practice is to include the most common search terms as “up and to the left” as possible. The logic behind this practice is (1) it makes it more obvious that a page is the most relevant result - and without relying on Google to grasp the relationship between the terms Wolverine and James “Logan” Howlett - and (2) it encourages increased click through since casual Marvel fans (i.e. search engine users) can tell it is the “right” result from a quick scan through a search results page.
That being said, none of the proposed naming conventions should hurt SEO (no alarm bells here!) and I agree that consistency is a beautiful thing. No matter the final decision, be sure to include links on the “main” article to each alternate universe article - and image galleries! - for that character. Strong internal linking reinforces the relationships between pages and helps both users and search bots find the right content.