Plug-In Comment Systems Suck
I do a lot of commenting on other peoples’ blogs, so I pay a lot of attention to the user experience for comments. In the last year or so I’ve been noticing the rise of third-party plug-in comment systems such as Disqus and Intense Debate. I understand the value of these systems (single sign-on, presence, control over comment content and ability to subscribe to discussions), but I always had concerns about the cost (not in dollars, but in terms of loss of control and reliability).
I host Wordpress on a server I own because I have this crazy notion that no individual or company should come between me and my printing press. Plug-in comment systems interfere with this by introducing a new point of failure into what should normally be a very straightforward process. Commenting isn’t complicated, but by using a pluggable remote system, you risk exposing your users to this:

(That 504 Gateway Time-out business is where Disqus was supposed to have been.)
There’s a larger trend at work here, the notion that a publishing system (or any software) is inoculated from gaps in its feature set because it happens to be modular/pluggable/hackable. This is one of the big lies of open source software (the reasoning is, if you don’t like the way it works, just roll your own). Wordpress owns Intense Debate now; they should roll its feature set into the core Wordpress product so I can host it myself and don’t have to rely on some disinterested third party to keep the otherwise very simple process of storing and displaying blog comments working.
That problem is exactly what this new version of Intense Debate is designed to address — graceful degradation.
Even if it works right 100% of the time, it’s still another moving part I don’t want to have to deal with.
The problem isn’t so much the third-party nature of the software but the fact that the data is stored on their server. The trend toward giant centralized databases creates single points of control that don’t exist with distributed, user-owned databases. The latter have single points of failure, but that’s something that could be fixed (e.g. with reciprocal backup peering with other small databases using synchronization).
Plus when the third-party vendor screws up or goes out of business you lose all your comments.
Jacob, actually with IntenseDebate on WordPress all of the comments are synced back to your local database, so if the service disappeared tomorrow all of your comments and data would still be there. :)