I've been working with multiple Multisite-installations where Authors need to embed Office docs from Skydrive using <iframe>s. This can't be done without giving 'unfiltered_html' cap to Authors.
Now that you have deprecated said capability, it makes my life a little bit harder. I also use the Unfiltered MU plugin, but that doesn't cover Authors.
So please, undeprecate 'unfiltered_html' cap.