It bugs me that they enable significant new features by default. At least with the portfolio dealio it is only "half" enabled. You still have to go to Settings --> Writing to enable the portfolios for real so I was able to deactivate the Custom Content Type module before it messed anything up on my site.

It's very kind of Automattic to make so many WP.com features available to the entire WP community. But I still don't understand why they chose to roll everything under the sun into one Borg of a plugin instead of releasing individual plugins for each feature.