One mechanic that would be neat would be the option to target armories for the ability to gain heavy weapons, which could be used to build and arm heavy troops such as MECs. They would likely be akin to targeting landed supply ships early on in Long War, being very risky, where even a success would include heavy casualties. Launching an assault would require a lot of preparation. You would need to find someone who knows the location of an armory, and maybe even someone who works at one in some fashion. Then you would have to obtain access codes, or get powerful enough explosives that it wouldn't matter. Next you could launch a diversion to draw away guards, at the expense of making the guards that remain more alert, or launch a stealth assault to catch them unaware. If you want to avoid attracting attention, you could try to sneak one or two operatives in, covering them with snipers, and just get a few light guns. Finally you have the option of doing a hot extraction with the skyranger or sneaking away into the city. The hot extraction would allow you to carry away more supplies, but might require you to target anti-air sites, and spend money on repairs. Running into the city would have you move less material, but would carry less risk.
Since you are no longer the reactionary force responding to alien attacks, you would have a lot more room for planning out assaults, and could pick and choose your targets.
Later in the game, it would be possible to just launch a straight up assault, using fighters to blast your way into the city. Such as option would give the aliens time to respond, so in addition the the guards at the armory, you would also have an elite alien task force responding to you attack.
Such a raid would greatly heighten security across the region, making a second attack neigh on impossible until it lowers, and even then it would be significantly harder. This would prevent you from just farming armories for weapons, and would make your choice of loot much more important.