Before get on with my personal reason's though, want to point you to Helen's December Post on the topic which is much more thorough, and a better guide if YOU are making this decision than my post will be (which is limited by the issues I find relevant to my situation and my miniscule knowledge on the topic).
Good Reasons NOT to Amazon
Counter: This is only my first book-- I have lots of books in my future to try to do better with. My eggs are not all in this particular basket, and an Amazon win would be a nice resume note.
Queries out there: What happens if, right after I submit, I get a request for a full? Even requests for partials I feel obligated to disclose on (or do I? Sheesh, what's the protocol?) And I do have that partial out there (plus the requested chapter)... two requests for more are thus far balanced by only two rejections with almost a dozen 'haven't heard a peep' still looming, and by submission opening, I am only 3 weeks out. Is that enough time to give those queries their chance to work? (obviously NOT, but were they going to work anyway?)
Counter: How likely ARE these queries to work... I mean really...
The Good Ship Amazon
Book Length: I've been wrestling my book length since the first time I finished this puppy, and I currently believe, for better or for worse, that about 80% of agents see ANYTHING longer than 120k and tune out. It's possible that I'm not getting that discrimination to the same degree now, but Amazon is a rare opportunity in being perfectly content to read such a high range of word counts. There will undoubtedly be longer books, and my long book, happens to not be as cumbersome as some long reads (at least I believe that's true).
Review opportunity: the opportunity to get feedback from within the industry is something I just haven't had an opportunity for elsewhere... sure you need to get past the first two tiers, and it's possible I won't—tier 1 is based on a pitch, and I feel like I'm getting there. Tier 2 however, is first 3k-5k words and I run up against my 'not quite fast enough first chapter' (though the criteria look like I should fare well—prose, character development... none of it mentions 'fast dive in' though it DOES mention hook) and if you pass those two tiers, you get feedback!... if you get to tier 3 you should get manuscript feedback. (in fact to ME, this might be considered 'winning'--getting this feedback but not being strapped with their contract. (though a sure thing contract is pretty darned nice, even at less than ideal terms—somehow I think Amazon winners sell at least a respectable number of books...)
So there I am, in a conundrum on the matter. I will probably remain in a conundrum until/unless I impulsively do something next week because I have a very hard time doing NOTHING and this contest entry is at LEAST doing something, and something that takes the whole thing off the table for a good long time at that. (which has definite appeal—being done for a while, I mean...)