Perhaps we should be talking less about a solution to the current system and more about a reaction to the current system. For example, dojos could react by offering their students a choice of receiving a dan promotion from Hombu (expensive) or from the head teacher of their dojo (inexpensive). Same test, same standards, same incentives to seek promotion, same bragging rights. The Hombu track versus the dojo track.
There might be a benefit to the Hombu promotion for a student who expects to move to a different part of the country (or world), or who hopes to someday establish a seminar practice. As for students on the dojo track, they would know that if they ever desire a Hombu promotion they will have to start all over again. Over time, the comparative value of each would be revealed.
I wonder if Hombu would allow such a system in a member dojo. Then again, maybe some dojos already do that.
As for the idea of some sort of independent accrediting organization, its first and perhaps impossible mission would be to define what is and is not aikido.
It's my understanding that Chiba sensei's organization operates under such a system. When he promotes people, he issues them a Birankai certificate for the rank, signed by Chiba. However, the student does have the *option* of paying the Aikikai promotional fee to get their rank 'certified' by the Aikikai. I have no idea how many of his students opt to do this. I personally don't think I'd bother. I mean, who's going to question a rank issued by Chiba sensei?