John Mueller of Google stated that Google ends up ignoring many of the EDU TLD links as they are frequently linked to spam targets. Google declared that the valuableness of EDU links is a common misconception and thus, they are common spam targets. So, Google tries to ignore more spam links in here compared to other places.
John posted on Twitter that the EDU links are link-spammed a lot because of the wrong idea about their value. Thus, a ton of those links are ignored. They should just be un-followed instead of Google having to ignore those.
In the earlier times, in and around 2008, all SEO wanted to pay up more for getting with EDU domain names. Only the accredited institutions and universities were able to receive the EDU TLDs and so, they looked highly valuable. However, according to Google they were actually not more in value. The question arises that to what extent were these student pages manipulated and spammed to lead Google to ignore these as a percentage, on the EDU TLDs rather than TLDs.
To sum it up, you must not go ahead and consider EDU links more valuable.
See the forum discussion at Twitter.