In 1999, the personal computer wasn't as common a household item as a microwave oven. It is now. Which means more people are trying their hand at writing a novel. Which translates to a lot of unpublished manuscripts flooding the market. I'm sure the policy of agented manuscripts only is a direct result of this flood. Publishers were needing someone to screen through the bad stuff before it could find its way to their desks and what better gatekeeper than a literary agent? So voila, there you have it. Unless the publisher is a very hungry small press, you're going to need an agent to get your manuscript read.
This is pretty much my analysis of the situation. A number of Internet developments have encouraged people to write, including the ease of disseminating fan/original fiction and challenges like NaNoWriMo. People writing is a very good thing. However, exposure to constant talk about getting agents and getting published, along with the relative ease of querying and submitting via email, may be encouraging premature marketing, flooding agents and editors with inappropriate submissions at an unprecedented rate.
I'm basing my analysis on all the posts I've read here, on NaNoWriMo and on other sites from people (young and old) planning to market first drafts or seemingly unpolished material. Pretty unscientific analysis, yup, but my impression remains.

I wonder if anyone knows of research or agent/editor opinion on this issue?
Anyhow, I wouldn't submit an unagented MS even to those big NY dogs that do allow it. The slush pile is a scary place to be -- you'll get a much quicker and less offhand read, from all I've gathered, if an agent gets you in the door. And I also understand that the etiquette is this: an agent should not resubmit a manuscript to a house that's already rejected it as slush.
Small presses seem to be another whole story.