First the Negative Upgrade cost Card.
The first Idea I had here is a EPT card that reduces a pilots PS by 2 and also reduces the cost of the pilot by 2.
IE Rookie Instincts (For lack of a better one) This is a negative squad cost upgrade card, decrease your pilot skill value by 2.
This would provide a way to reduce the cost of some pilots that have middle of the range pilot skill but see no play time because they are just too expensive.
Second Upgrade kit.
My idea here is a kit that does not have a plastic ship but contains upgrade card(s) with adjustments to an existing ships dial.
As an example a kit that has a new dial for an X-Wing that includes a 3 Sloop and the associated title card that changes the dial.