I wouldn’t argue that the ending of the film was the very best way of ending it, and probably another auteur interested in genre-exercise would have come up with a cleaner or subtler execution. But considering the source material, the stakes were really too high, and the buildup was resultantly too extreme for a gentle comedown to occur. The comedown turned out ridiculous because the patient was obnoxiously obstinate to live in his carefully constructed noir-world. I was inwardly chuckling at Ben Kingsley’s extremely annoyed face as he explains for the umpteenth time the “truths” that DiCaprio continually represses inside himself. The Dan Brown-esque chalkboard writeup, the anagrams, and the pedantic reduction of Teddy’s whole trauma in under 5 minutes, might come off too heavy-handed, but from what I understand, the ending of the film very closely parallels the ending of the novel. With this in mind, I’d say the source material would be at fault for the “clunkiness” the film is accused of: Scorsese merely translated into catatonic prose what was already gothic pulp. I haven’t read the book, never read Lehane, but I’ve gathered that there’s very little deviation from the original:

http://blogs.indiewire.com/thompsononhollywood/2010/02/24/dennis_lehane_talks_shutter_island/

One review of the book (written long before Scorsese made the film) even puts it this way:

“The driving tempo of this novel seems to evaporate by the end, like the calm after a storm. Lehane drops plenty of clues for his readers, as he leads them toward significant shifts of direction and perspective. However, the big twist on which Lehane’s tale ultimately turns is more likely to incite a shrug than a shock. What was once pertinent and compelling is turned into a type of parlor-trick emptiness.”

http://januarymagazine.com/crfiction/shutterisland.html

In regard to its “exploit[ing] a historical awareness of the viewers” and making a “mockery of such endeavors to absolve oneself of the world’s monstrosities through truthseeking,” I find the film to be as serious about real-life conspiracies and the horrors of the holocaust as “Night of the Living Dead” was about racism and lynching. I personally didn’t find Scorsese overly interested in allegorizing, much less mocking, these real world atrocities in a way detrimental to their prevention or impedance. If anything, Scorsese/Lehane were in search of making sense of a horrific event(s) through the multiplication and disorientation of the protagonist’s social identity, by way of the “Atrocity Exhibition” medium employed by J.G. Ballard: incidentally, a collection of stories (Ballard calls them “condensed novels”) that are narrated by the shifting personalities of a doctor at a mental hospital whose psychosis stems from ‘outside world dread’ — the hydrogen bomb, the assassination of John F. Kennedy, the “suicide” of Marilyn Monroe. Like in “Shutter Island,” the audience/reader is helpless to know which narratives are truth and which ones are fictionalized by the protagonist, because both the ‘truth’ and its fictional counterpart turn out equally unbelievable. The hydrogen bomb and the Tuskegee syphilis experiment would be horrendous absurdities if they hadn’t really existed — but they do exist, they did really happen, and a kind of madness (cognitive dissonance) is incurred by this realization:

http://en.wikipedia.org/wiki/The_Atrocity_Exhibition

I thought it was a lovely film, for all the reasons you articulated better than I ever could have. But I, as viewer, couldn’t help feeling betrayed by the film for those same reasons. As an acquaintance of mine recently put it, the film “abuses your willingness to suspend disbelief.” It exploits the historical awareness of viewers who, with the best of intentions, have become familiar with the real-life conspiracies that are mirror images to the film’s delusions – those who hope that “keeping up with the news” and reading about cointelpro / the tuskegee experiments, etc. will somehow railroad future atrocities. To the extent that the film makes a mockery of such endeavors to absolve oneself of the world’s monstrosities through truthseeking, it was a disappointing and bitter ending (although by no means dumb).

Also, a question:
Why do you think the delivery of the “surprise” was so clumsy and hackneyed? By which I mean, why the super lame addition of the anagram names on a blackboard, literally revealed when the sheet is pulled off it; why the crumbling gun and the cliche “office” in the lighthouse? Clearly purposeful, but I have trouble fitting it into your analysis.