Here is a great blog post about the transition from WP to EE written by one of our designers - http://www.viget.com/inspire/wordpress-to-expressionengine/
and here is another unique EE site that shows the flexibility of its native theming system -
Template processing is slow, processing order is wonky, and it's very easy to create N+1 query loops that can only be avoided by writing custom SQL queries/php. They also made some poor database structure choices in certain areas.
Mostly though it just boggles the mind why they put so much effort into creating a regex-based templating system when the app is already just PHP.
Still, probably the best CMS I've used and it certainly has its uses. I just wouldn't use it to develop anything complicated ever again.
Might want to revise that to "from WP to EE."