A key reason is mentioned on the WP-Testers list by Ryan Boren, one of the developers:

“The big schema change is the dropping of the categories, post2cat, and link2cat changes in favor of the new terms, term_taxonomy, and term_relationship tables. Any plugin that queries against the old table will break horribly.”

What this means is that the new WordPress has shifted its data structure from a category-basedsystem to a new taxonomy.

If you’ve extensively used category-based plugins to enhance your SEO or social marketing efforts, you’ll bang into lots of error messages, as anyone who’s posted a comment on this blog will attest to.

Given the number of social-based plugins I’ve installed, and the extent to which they interface with the old (now defunct) category-based data strcuture, you can expect to see lots of errors like “WordPress database error: [Table ‘blog_wrdp24.wp_post2cat’ doesn’t exist]”

Even better, I don’t receive email notifications of pending comments now…

So, it’s no wonder that some have called WordPress 2.3.1 the “blog plugin killer”

It does represent an evolution of the blogging platform, with the inclusion of native tagging support, although many bloggers have commented that it’s doesn’t hold a candle to mature tagging plugins like Simple Tagging and Ultimate Tag Warrior.

Still, it’s early days yet, so keep your fingers crossed that that WordPress development team will launch their own plugin enhancements or an incremental upgrade soon.

For more information, you can check out this WordPress.org thread.