If there is consensus that there is no deliberate InterWiki Map favoritism, then the only concern is to prevent the appearance of InterWiki Map favoritism. This could be accomplished by clearer criteria for InterWiki Map inclusion.
For instance, a short paragraph at the top of http://meta.wikimedia.org/wiki/Talk:Interwiki_map could do the trick. In fact, a simple paragraph of explanation is currently curiously absent from the InterWiki Map.
I'll take a shot in the dark here:
INTERWIKI MAP CRITERIA FOR INCLUSION:
"The InterWiki Map exists to allow a more efficient syntax for linking between wikis, and thus promote the cooperation and proliferation of wikis providing free information on the internet. Sites considered for inclusion should probably 1) be a wiki 2) be a free content site 3) be reasonably developed 4) be trusted not to produce spam links and 5) provide a clear and relevant value to the mediawiki community.
The process for determining inclusion is similar to [[AfD.]] Members of the community may present pro's and con's, with a Meta administrator determining consensus and acting accordingly.
Sites included in the InterWiki Map are considered to be trusted sites by the MediaWiki community and thus "nofollow" is removed from InterWiki links."
A short paragraph like the above could be sufficient to assuage the concerns of those who suspect Wikipedia/Wikia nepotism. This sort of fix may be all that is necessary to quell concerns of a Nefarious Wikia Conspiracy!