Ok, first off, allow keyboard & mouse customization for the Windows release. Seriously, I am VERY upset that people who buy it from Steam get to customize their controls, but the ones who are LOYAL and buy it from Microsoft do NOT get to edit their controls. They are simply not comfortable for many people, and one of the main advantages of PC gaming.
Next, allow for multiple skulls to be active, instead of just two, AND have check points AND have the Easy-Normal-Heroic-Legendary difficulty settings.
Finally, add reloading and having to replace plasma/ beam/ laser weaponry, instead of every weapon just having one single clip of large ammo.