[CraazyCanuck]

If they had an air base they could introduce AA placements located with angles to cover underneath the base as well. And perhaps introduce missile based AA similar to what we already have now on the Lib.

This could also allow specific missions for air to complete. Think Star Wars and the Death Star sequence. The developers could introduce a high payload missile or specific nanite payload that aircraft need to deliver into crucial and highly defended areas on the base. Delivering these payloads would have significant impact on the capture of the base. They would have to forgoe their secondary option on their esf for this payload.
Some examples:
Open the way for ground forces to access the facility from below.
If/when they bring in automated turrets, they could allow air to shut them down.
Shutting down shields in areas that would allow air to fly in or drop troops into the facility directly.
Taking out radar and Electronic Countermeasures of the facility.