Writer's Fallout Shelter

This may come across as a bit harsh, but here I go.

First, I agree with much of what Rebecca said. The query letter is too long and contains a great deal of irrelevant information. The first time I read it, I found myself starting to skim around the third paragraph. You also speak in a roundabout style. By roundabout, I mean such phrases as "I call this novel..." It makes you sound uncertain and as if you are hedging. Don't hedge. Be confidant. Be self-assured. Be direct and to the point. Don't waste words. They're precious.

Now for the harsh part:

My name is Christopher Kohls [1] and I call this novel An Account of the Life of Thomas Stuart. [2] I believe it is particularly suited to you as a literary agent. I would like you to take the opportunity to review my manuscript and consider representing me, this work. [3] I am currently writing a second novel, completely unrelated to this one which I would hope to sell through your service as well. [4]

[1] Is your name listed somewhere else in the letter or is this the only place we can find out this information?
[2] You call it An Account of the Life of Thomas Stuart implies that other people call it other things. Just give me the title straight out.
[3] Of course you think it is suited to the agent and want them to read it and consider representing your work. Why else are you be querying them? If you want to include something like this, it is better to be specific. Why do you think they are suited for this work? Individualize and personalize the query.
[4] What does this have to do with the query for this novel?

The story I submit to you here is the struggle of one man to make his fortune through the dangerous game of espionage while leaving some time for his fiancé who knows nothing of his “employment.” [5] We see Thomas [6] adeptly maneuver from his personal life to his career and we focus on a vast spectrum of American society and of the world of espionage. [7]

[5] This sentence reads like a maze. This is the point where you started to lose me.
[6] Who? This is the first time you've mentioned your protag's name.
[7] This sounds like a lot of movies I've seen. How is your novel different from them?

At the time of the novel, all is well in the United States. We have our political debates and not everyone is happy, but we are in a time of relative contentment, and news tends to focus as much on the preverbal “cat stuck in the tree” as it does international crises. [8]

[8] I was a little confused with this paragraph. Although you say "at the time of the novel" I get the impression you've switched from talking about the query to your perceptions of real life today. Also, I don't really care at this point.

There is some tension, [9] however, in Europe concerning the massive influx of Muslim immigrants. One man, power hungry and twisted, sees this fissure and uses it to secretly rile the population of that continent into an organized rage. The man’s name is Samael.

“He was like a great bird of prey, or perhaps like a mammalian predator, or even a lizard. Whatever the case, he was classically beautiful, and terrifying to meet. He often referred to himself as “the Venom of God,” and so it was known throughout the Kafres organization, and the title struck fear into just about all [the men].”

After years of peaceful protests, and watching as nothing seems to be going their way, Samael finally decides that it is time to strike. He poses a plan to the organization he has developed,

“He let them talk a lot longer this time. He acted as though he was called away and tending to a matter, but in truth, he was allowing the fantasy to swim in their minds [....] First they would condemn the idea aloud while selfishly desiring it privately, and then someone would say something to justify it, something that would click with the man next to him, and the man next to that man [...] and so they would be in unison in their delusion, in their justification of the evil they were about to permit.” [10]

[9] I'm not sensing any tension.
[10] This is reading like a synopsis, not a query. A synopsis is a separate document. Also, as a synopsis, I'm not finding anything too unique here. There's nothing to distinguish it from similar stories. What makes your story different?

I have written here a projected history of the future using one character as our guide. [11] I pose some philosophical, psychological, and political questions that I don’t necessarily answer. [12] I draw the reader toward consideration by taking ideas to extremes and giving characters absolute and well-considered points of view. [13] [14] My manuscript is 120,000 words.

[11] Sounds like you believe you're prophesying the future. I'm not interested in predictions. I want to be entertained.
[12] Does this mean you leave storylines hanging?
[13] Wording is convoluted.
[14] I want to be entertained, not educated.

I believe that, if properly marketed, this book will be well received [15] by a wide audience, those wanting the thrill of an adventure epic and those who want to contemplate more profound questions. [16]

[15] There's an implied insult here that indicates if the book does not do well, it will be all the agent's or editor's fault for failing to properly market it. Books don't do well for a variety of reasons, most of which are out of the editor's and agent's control. I'm also going to avoid working with someone who appears to have this mindset.
[16] Who is this audience? What else have they read and enjoyed?

I thank you very much for taking the time to read this letter and I look forward to sending you my manuscript upon your request. [17]

[17] This is a given.