Variable lighting - it would be cool if, for example, interiors of UFOs or buildings without windows were dark inside, with reduced visibility even when mission takes place during the day. Or the other way around, visibility is 100% in well-lit buildings during the night missions.
Weapon customization - for example, an assault rifle could have couple slots for additional equipment - flashlight, additional grip, laser sight, 40mm grenade launcher, something like mini-shotgun attachment or what have you. It would make the weapon more versatile and could create more tactical options during combat.