System fonts have been painstakingly hinted to make them more readable on-screen. Most web-embeddable fonts don't have appropriate hinting or are just plain bad choices for body text. Hoefler & Frere Jones (one of the most respected foundries around) haven't released embeddable fonts because they've been working on it for years.
The result is fuzzy text at small/medium text sizes. It's huge pain to read. It seems some designers forget that good typography is concerned with readability too.