Edit: lol, I participate in a lot of contentious threads here, but this simple question where I am genuinely trying to understand something has generated the most downvotes.
Reddit is precariously close to doing a 'Digg'.
It wastes too much screen estates for no reason. On my screen about half the width is wasted on the left and right blank spaces.
It breaks a lot of subs' custom theming.
The comment section navigation is horrible. It only shows comment maybe 5-6 level deep and if you expand then you will have to "go back" later. When you first go into a thread, it also doesn't show all comments, and instead requires an additional click to "View entire discussion".