There are certain ship/upgrade combinations that create an NPE and ships with upgrade slots that never get used because adding the upgrade is not cost effective. The current point adjustment method can't fully address these cases. If an upgrade is costed to high to rein in one specific ship pairing it hurts every ship that take that upgrade. Conversely if an upgrade cost is lowered to much to help encourage its use on one platform it could completely break another platform.
To address both of these instances I propose introducing upgrade specific cost modifiers for ships and pilots. These modifiers would be indicated as 0-3 arrows next to a ship's upgrades. The direction and number of arrows next to the upgrade would indicate the point modification. For example the TIE Advanced x1 could have one arrow up next to its system icon and two arrows down next to the missile icon, indicating that any equipped system would cost one point more and any equipped missile would cost 2 points less. Furthermore Vader could have two arrows up next to the modification upgrade.
In addition to the cost modifiers there would have to be a few other items to consider: should certain upgrades could be marked as non-modifiable (free R4s or Contraband Cybernetics sounds like a bad idea), should negative upgrade costs be allowed, how would cost modification work for double upgrade slots?
I think adding this ability to modify individual upgrade costs for ships and pilots can help address certain toxic combinations (Juke/Phantoms, Adv. Sensors/Guri) without over penalizing other ships that would use those upgrades. It would also allow ships that are not usually cost effective with upgrades to become more viable (ordinance carriers).