Making actual controllers accessible

I have discovered elsewhere in the forum how to hack index.php in the root directory to make normal CI style controllers accessible through the url (BASE_URL/controller_name/method_name) by commenting lines 97-99.

I have 2 concerns with this:

1) What can I expect to be broken with these 3 lines removed? As far as I can tell, the routes file is ACTUALLY used if you comment them, so basically if there is a match to a controller/method it will go there, else it will look for a match in template-group/template, else it’ll throw a 404. Are there any issues that I’m missing here?

2) I’d like to have this functionality without actually changing anything inside of index.php to avoid potential problems in the future if/when we upgrade EE. The best I can come up with is to write a EE_Router and overwrite the _set_overrides() method to not actually set any overrides. Though, this seems inelegant (and that’s putting it nicely) - is there a more reasonable way to approach this?

Thanks in advance for any help/comments!

edit - figured out what I was doing wrong with MY_Router thing, doh! Rest of the questions are still relevant.