I'm choosing to use another engine because this engine does not have destructible environments natively. Basically, what I'm envisioning right now is your squad gets dropped into an area and move around finding and fighting the aliens like a typical rtt game. You would have cover that can be used, special gear-related abilities like suppressing fire and jump jets. Weapons would have multiple fire modes. The squad would be sub-divided into smaller groups that you can set up in advance.
For example:
Your assault team can be sub divided in 4 smaller groups (Alpha, Bravo, Charlie, Delta). So I can have my sniper in one group, a scout team in another, general purpose assault group, and a heavy weapons group. How you create the groups are up to you but each group is limited in the number of soldiers it can have (say 4). Each soldier can also be given a kind of role in the group through action scripts. So in the assault group, I may have 2 rifle users, 1 machine gun user, and 1 medic. I can set the medic to use a "medic" script and that soldier will heal first and attack second. There will be no classes per say, but different items may have different abilities associated with them. For example, a machine gun set to firing full auto would be able to suppress the enemy. Each unit can fire for X seconds and then they have to reload, costing Y seconds. As previously stated, each weapon may have multiple fire modes, ranges, and accuracy ratings, so you can do something like aimed shots (takes more time, more accurate) or burst fire (short bursts of bullets, less accurate) or full auto (continuous fire, very inaccurate, can suppress).
In combat, you can move the sub-groups around as sub-groups, you can move units around individually, or you can hotkey your own groups. Cover will play a role so you can take cover behind objects. Movement would be more important. For example, if my scout group encounters the enemy and they start exchanging fire on a ridge. I can move my assault group, with their flying suits, behind the enemy group. In this case, the flying suits are like the jump jet units in games like C&C. For buildings, I think I'll just have building occupiable. When your troops enters a building, they'll take X seconds to secure it. If enemy units are in that building, a fight would happen during those X seconds. After all is done, whoever is still alive occupies the building like in traditional RTS games. If an enemy unit enters a building that has a civilian, the player has Z seconds to get units in there to stop them or the civie dies. I have yet to really figure out how to do terror missions.