A substantial disadvantage of semi-colons is simply that they're rare. If a small but significant portion of your readers don't read them as you intend you're better off finding another way.
It's a pity though, because if I were writing for perfect clones of me, they'd often be the best choice.
I use semicolons a lot more when writing on Less Wrong (and other places where intelligence is high) than on many other places.
Update: Discussion has moved on to a new thread.
The load more comments links are getting annoying (at least if you're not logged in), so it's time for a new Harry Potter and the Methods of Rationality discussion thread. We're also approaching the traditional 500-comment mark, but I think that hidden comments provide more appropriate joints to carve these threads at. So as of chapter 67, this is the place to share your thoughts about Eliezer Yudkowsky's Harry Potter fanfic.
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six. The fanfiction.net author page is the central author-controlled HPMOR clearinghouse with links to the RSS feed, pdf version, TV Tropes pages, fan art, and more, and AdeleneDawner has kept an archive of Author's Notes.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: