I was thinking if it would be cool to add Alien HeadQuarters in the Inner Core which contains guns and probably other stuffs and the only way of getting them are by destroying these HQs. Also these HQs could be protected by a shield and the only way of taking down the shield is by destroying its generators and then the whole base. It would be also cool if a lot of alien strike waves respond to this attack as well(fighters , BSs, Motherships... everything).
The expeditions could be done by a specific time when the HQs are in the Inner Core ( like 1.7 with the DK gate in Altair)... or maybe this time it might be cool if the HQs are in the Core everyday.