you could use phpMyAdmin to do a search&replace on the wordpress database for the old youtube embed string and then replace with the new one. Should be possible since the syntax is similar enough.
edit: to add from this other stackexchange question:
Search RegEx is a good plugin to be able to search and replace with Grep through all posts and pages. With that, you can change your shortcodes to the default Embeds « WordPress Codex that self-hosted WordPress uses, which in its simplest form is just the URL.
Or use WordPress › Viper’s Video Quicktags « WordPress Plugins and search/replace to convert to that form of shortcode.