My conjecture:
The concept of the arguments object has been on the language since the very beginning, it’s even described in the ECMAScript First Edition Standard(PDF).
In that version of ECMAScript, the Array.prototype was really basic, array objects contained only 4 methods!: toString, join, reverse and sort.
I think that’s one of the major reasons about they make arguments to inherit from Object.prototype, at that time those Array methods didn’t look too useful.
But the Array.prototype object was extended in the next versions of the standard, now on ES5, Array objects have methods such as map, reduce, every, some, etc, that are really powerful.
The last year, there was a proposal in ES5 to make arguments inherit from Array.prototype, in the draft stages of the standard, but was dropped off time later.
In those drafts, arguments inherited from Array.prototype, but for backwards compatibility with ES3, the arguments object had defined two own properties, toString and toLocaleString, both pointing to the same methods on Object.prototype, but finally, the committee decided to keep inheriting from Object.prototype.