I see two issues with AngularJS application regarding search engines and SEO:
1) What happens with custom tags? Do search engines ignore the whole content within tho
Update May 2014
Google crawlers now executes javascript - you can use the Google Webmaster Tools to better understand how your sites are rendered by Google.
Original answer
If you want to optimize your app for search engines there is unfortunately no way around serving a pre-rendered version to the crawler. You can read more about Google's recommendations for ajax and javascript-heavy sites here.
If this is an option I'd recommend reading this article about how to do SEO for Angular with server-side rendering.
I’m not sure what the crawler does when it encounters custom tags.