The only other thing would be that somehow legacy armor is costing more, and that there is truth that a fancier shell is equating to cost, even though there is no performance gain.
I just did a quick test. The legacy armor shell does cost more. Probably because the inherent cost to purchase makes them have a higher value. I tested dieing with only 1 piece of gear on. A head piece.
I tested it with the Agent's Exalted Headgear and with a Synthmesh Battle Headgear. I tested with and without mods (enhancement and mod were 23s and the armor was 22). I ensured both pieces of gear had the same durability for the same test.
Legacy Exalted Gear (90/100 value 8385) - 838
Synthmesh (90/100 value 580) - 58
Legacy Gear (89/100 value 13285) - 1461
Synthmesh (89/100 value 5480) - 602
My guess is they added the cost of the shell back into the cost of the repair, whereas before it was just the cost of the mods that were the repair cost. Expensive shells (I believe the legacy gear is over 1 million for the level 20 gear set) are costing significantly more to repair now.
I would also theorize that the more expensive the mods the less the shell cost weighs into it. For example I tested with a set of generic mid range mods and the values were:
Legacy Gear (90/100 value 9005) - 900
Synthmesh (90/100 value 1200) - 120
So the values of the objects get closer together as the mods become higher valued (which makes sense).