I'm surprised to see this question raised here. I raised the same issue on a Wikipedia project talk page & practically had my head handed back to me for it.
I think it is -- or will be -- a problem because of Wikipedia's growth. Once upon a time, everyone on Wikipedia knew who Jimbo was; if you had a problem, you could email him & get a response in a reasonable time. Now the community & the projects have grown, & there are a growing number of active contributors who have at best a vague idea who he is; unless you happen to be someone who is uppermost in his mind, it may take him as long as a month to respond to an email. (This is not a criticism, just a statement of fact: with everything he has a part in, I can understand that some people don't get as much attention as others.)
Due to all of this, I can forsee the day, may as soon as 2-3 years down the road where enough Wikipedians don't know Jimbo, start considering him a troll or a fossil that is limiting Wikipedia -- & stage a coup. (I laid out a vague plan of how it could be attempted on that Talk page, which might work for a few days until someone went to the colo & powered down the servers.) This effort to depose the "God King" (a label I wish had never been coined) would most likely be unsuccessful, but that will rob us of time & energy better spent on our project, & likely alienate a large number of good contributors.
If a formal relationship between the various Wikimedia & Jimbo Wales was defined -- say that he is considered ultimate arbitrator of all disputes -- it would head off that potential problem. I think that statement fairly describes the status quo, & gives him no powers that he doesn't currently have. And if, years down the road, many Wikipedians don't like that relationship, it would lead them to seek a change by negotiation -- not a coup.
Of course, Jimbo's best solution for dealing with the growing distance between him & the average Wikipedian is to travel & meet more -- which he is doing. But Jimbo is one person, life is short, & the number of Wikimedians is great. Defining his relationship with (at least) en.wikipedia would give him more time to continue this work.
Geoff