Use the existing upgrade trees, with special "modification engrams" that take the place of an existing spot on the upgrade tree. They would get permanently attached to the weapon or armor and take the place of the existing slot (example: your assault rifle has "fires slower when zoomed" and you get a modification engram for" extended magazine" equipping it in the" fires slower" slot replaces that ability permanently. With this addition, we could still use existing weapons without modification (on the player side, I'm not a programmer and have no idea how difficult this would be) but would also have the customization many players are craving. This would also give us something new to look for in engrams. Oh and on order to replace an upgrade on the upgrade tree you would have to have purchased the standard upgrade before replacing it with the mod engram.