Two ideas

[Blackhorn]

• 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.

[Rhishisikk]

Or if there were actual light switches in the buildings.

Second on the ability to refit/mod weapons.  Give the engineers something to do between big projects.  Or just let the soldiers do it themselves with a pool of "mod points" based on XP and research.

Or an Armory building specifically for weapons tweaking, building, and research.

[RustyNayle]

I think standard rifles should definitely have at least one mod spot.  This would allow the fitting of a silencer / suppressor, bayonet, flashlight, telescope, laser sight, high cap mag, etc, depending on the type of weapon.