Which is why you do agent research, find out what agents want, and give them that. Sure, you can sell a book that bucks the system, but that doesn't make it the SMART way to get a book published. That's why I said plan on being the rule and not the exception.
It's so unbelievably, ridiculously easy to get rejected. Why on earth would you want to give an agent an instant reason to reject you? Length will hit in the query letter. They won't even GET to your amazing, singular, one-of-a-kind, once-in-a-lifetime manuscript. They'll see, "This story is a completed alternate history novel of 210,000 words..." and hit the auto-reject button.
Let's just take one agent (my first-choice agent), Jennifer Jackson. She's Jim's agent, btw. She keeps a blog and very kindly posts the stats on how many query letters she's read in a given week, how many requests-for-partials she's sent out, what genres they were in, etc. I'll go back a post on her blog, since this past week she was at a conference and her numbers are a little off for her, but here's what she posted for the week of 5/7/2010:
# of queries read this week: 268
# of partials/manuscripts requested: 1
genre of partials/manuscripts requested: YA
400+ queries awaiting review
oldest query in the queue: 4/12/2010
ONE partial requested, out of 268 letters she read. ONE.
Now, you can go ahead and buck trends if you want. Against those kinds of odds? I'm doing everything humanly possible to make my first novel publishable. I'll write my 250k word epic later, once I've established some cred.