This mod has improvements for all aspects of the game: from weapons and enemies to physics, not to mention the game's main menu and even the map.
The amount of changes is too big to list in this description, but to give you an idea, the damage and effects of each weapon has been improved, artificial intelligence fixed, enemies are more resistant, there's more blood when needed (missile explosions, etc), and both the games graphics and sounds have been vastly improved.
On this last point, we should mention that not only do the graphics stand out much more than in the original version, but they don't affect game performance.
Perfected Doom 3 is an essential mod for anyone looking to play iD Software's classic game today. Not only is it much better graphically, but it also offers many additions and improvements. It would be a crime to miss out on them.