Actually, it's not quite as huge as it seems - at least not any huger than any other musical subject. And, as with any other musical subject, there are already some very thoughtful, interesting, and varied approaches to sequence of learning, though with some carryover from one to another, most of them starting with what are seemingly the very fundamentals of music. So, I don't think the question is exactly right - I think it's more personal than that.
The funny thing about theory, for the most part, is that the expectation is that each student will learn it and know exactly how to personally apply it to their everyday musical experiences and endeavors, while at the same time it's treated like an absolute subject and as though there is one, methodical application which everybody should learn about in the same way, in a classroom setting. Well, there are pluses to that and there can be benefit, but there are also negatives and most of those centered, I think, on the fact that it's not an absolute subject which can be learned about (nor "should" it actually be) in a single, methodical way. What is lacking, as far as I can see, is the kind of private and personal instruction and guidance that an individual receives in instrument study, in knowing how to really grasp musical(/theoretical) ideas in a personally meaningful and practical way (as in, not as a separate subject but one which directly applies to instrument/musical study).
And, why shouldn't it be treated that way? We certainly don't expect to learn everything we need to know about instrument study through classes taught from books and methodologies, and if there is anything under the sun that is truly applicable about theory to our personal study of music, then in fact our understanding of it will necessarily grow and develop in very personal ways! But I digress (actually, I just wanted to try out saying something like that ... "but I digress" ... it sounds pretty great for certain situations, doesn't it?

).
Anyhoo, basically, I think there is already a very nice backbone, but it needs individual attention and supplementing in order to create a true atmosphere, environment, and pathway for personal understanding. I think it's expected that each individual will just kind of do this after they've taken classes ... if they want to or feel inclined, and I don't argue that this is needed, just as it's needed within any musical study and endeavor.
However, I think that based on what seems to be the trends, it's clear that there can be some adjustments. What I mean is, there are some people who 'get' theory as a subject in and of itself, and they can apply it to notes on the page and even to technique, but the meaning behind the music while performing can be lacking. And then there are people who don't get theory at all and who find it pointless and/or meaningless, or are just struggling, while these people's abilities to be
musical and even technically proficient, can be very high. In other words, there's often still a gap between "the subject of music theory" and then the actual act of music making. As far as I can tell, ideally, all would be one, whole, working musical expression.