I honestly wish there was a major recurring antagonist in the series....
Also, for the love of god, SR5 better be released alongside modding tools and proper support the same day it hits PC, because obviously it is a pain to shoehorn modding into the SR2-4 a long while after release when they were never originally intended for such.
Instead of straight tiered upgrades for weapons, give us a higher degree of weapon customization, like adding attachments and modifying internals to boost stats.
Character customization should have super intuitive ways of modifying every aspect of your character. Let us put hair wherever we want, let us deform our characters in every which way, let us paint skin colors on with our mouse instead of choosing one solid color, unlock all sliders so we don't have to do that ourselves, etc.
Finally, I hate how open world games like GTA and SR have tons and tons of buildings that are nothing more than trees in the urban jungle. Every building should have an interior. Heck, that might open up some neat diversion possibilities, like burglary and home invasions.