For the most part, this plugin works well. But I have a WordPress site that has /index.php/ in all the links, and the canonical URLs don't work for the archive pages. Instead of /index.php/page/2 it suggests /page/2, which doesn't work. I haven't seen this issue with posts or category pages.
I've got a redirection in place to avoid 404s, but this likely isn't great in the longterm, for SEO reasons.