This is probably going to sound trivial — and it is — but my main complaint about WordPress.com is its name. It is tremendously confusing to people, including WordPress users, WordPress.com users, and outsiders. The WordPress.com forums are full of people asking things about WordPress, and the WordPress project gets “collateral damage” flak for WordPress.com policies. It also hasn’t helped the issue of people thinking of WordPress as a creation of Automattic, instead of the other way around. “WordPress” is entered into web award competitions, but it often is clear whether they mean the WordPress project or the WordPress.com service. I can’t help but think that both entities would be better served had the WordPress.com service used a different name/domain: [FooName] — powered by WordPress.
I’ll now open the floor to Lloyd Budd for a counterpoint. :-)