Whats the big deal with index.php? Why do some EE developers go about removing this? What advantages / disadvantages does one have when removing index from EE?

Everyone has there own preference to this but I prefer to remove it. My main reasoning is that the URL’s look cleaner and are easier for your web site visitors to remember. Also, when your pages are indexed by search engines, your URL is displayed. Potential visitors look at the URL and I think a cleaner URL that is descriptive information about the page content is more appealing than unnecessary clutter.

The only disadvantage of fixing it is that it can on some web hosts be a little frustrating particularly for those with less experience in setting it up correctly.