What was Akamatsu Ken's role in creating Negima!? Neo?
I'd say that the info on MAL's page would be the accurate one.
You can see in Amazon's page for the first volume of Negima!? Neo, that both the information on the authors (right under the title) and the cover state that the story is by Akamatsu Ken and that Fujima Takuya is the illustrator.  

  

Also, Amazon.co.jp's page on Negima!?Neo too states Akamatsu Ken as the author (赤松 健 appears under the title followed by the kanji 著, which means author).