[eluser]kgill[/eluser]
On their own web apps suck for interactivity, and that's where the wonderful world of Javascript comes in, specifically AJAX. Look into jQuery, that will give you a lot of what you're used to being able to use (events, modals, updating forms based on user action and so on). What you essentially will end up with is CI/PHP on the server side handling the processing and jQuery running client side enhancing the UI. Ideally you want to write your app so it works if JS is turned off (graceful degradation) but if you couldn't care less about the non-JS users then go to town with all the UI stuff. jQuery is of course not the only javascript framework out there (just happens to be my preference) you could also look at mootools, Dojo, YUI plus a bunch of others.
