I agree Vallee's "system" is vague, but I think it's vagueness is part of its appeal (to me). I probably will horribly mangle any attempt at a synopsis (his book "Dimensions" goes into it), but the control system hypothesis basically differs from most other explanations in that it assumes the minimum "known" facts about UFO's (again, this is just my personal opinion).
Basically, all we know about UFO's for certain (I'm sure there are plenty who will debate this) is that they, as a phenomenon, affect us (ie, people). Accordingly, we react to the phenomenon. Because we react to them, we are changing as a society, although how and at what pace is unknown (but perhaps the most objectively quantifiable aspect of UFO's). This suggests some system, intelligence, or other 'controlled/controlling' mechanism, but beyond this we can't say whether they are from outer space, our collective psyche, another dimension, or wherever.
I like this view because of its minimalism and empirical grounding. It's also a sociological point of view, which I prefer to the "nuts-and-bolts" type of views (which I think are limited and what Vallee would probably label under the "physical" aspect of UFO's), but at the same time not as purely phenomelogical as the bulk of modern abductee research, which seems at the other end of the spectrum (ie, very subjective and often highly speculative).
An added benefit of Vallee's ideas (to me) are that they adapt themselves very well to manipulation of the UFO phenomenon by people, be they governments or cults or whoever, for other motives. By exploring UFO's from the starting point of 'how do they affect people' rather than 'what are they' or 'why do they do what they appear to be doing to us,' one can gain a much greater idea of the scope and nature of 'human' manipulation of the phenomenon. (In this regard Vallee is one of the most penetrating and insightful skeptics I've ever read).
Well, that's my attempt