When a piece of armor is masterworked two armor perks in the same column could be activated instead of one.
A helmet with Light reactor and Scatter projectile targeting in one column. Fusion rifle reserves and rocket launcher reserves in another column. Both columns could be completely activated or only one column of perks depending on the level of the masterwork.
This idea would give Guardians more power in all activities. Masterworked armor would have greater meaning in this game. Masterwork cost should remain the same so all player have chance to upgrade their armor.