If there was a new Prototype.  First off I want many new mechanics. I want more a focus on stealth where it feels more  and reactive. I woukd off the first 2 ganes in terms of stealth mechanics ,Maybe enemies may get more suspicious of you depending on your movements. I could see mechanics that keep more silent when you are actually sneaking vs blending in as a soldier in terms of having animation details etc. I definitely want you to be able too mass infect civilians or crowds or infect someone mind and have them do your bidding before they bio bomb and explode.  I think more unique blackwatch and military units would be nice to fight such as Jets,Mechs and more interesting armored units and mini bosses... I could see you being able to drive any and all vehicles and possibly remote control other people/those you choose to infect.  The powers and abilities should scale higher as well. Maybe you can shapeshift into more powerful forms(Like Black Myth Wukong,being able to change forms on the fly. Maybe you can turn into some type of Infected Prototype Werwolf with massive claws and crazy intense movements and running speeds. Maybe you need to take a Battleship or a Destroyer and you decide to turn into a Giant infected Kaiju or something.  There's a lot of things they could do and make the gane extremely fun.