wpmnger – you’ve always needed to use PHP mode or legacy mode for the dynamic content functionality, so there’s no change there.
I would say stick with the ajax calls or use a more granular caching system. A full page caching plugin like WP Super Cache or W3 Total Cache cache the whole page. If you use an object cache like memcached or any of the mysql caching plugins on wordpress.org it might be easier to keep parts of the page dynamic.
Having said that, the filter based system here works well and I’m happier about it than the old eval() method which wasn’t that secure.