Agreed, any weapon that is only available by crafting (for example mk2 flamer) is pointless to repair because it needs another crafted mk 2 flamer and at that point you already have a fresh one.
The current system is okay once you have at least two 70/100 items. By repairing what you have, it delays your need for crafting a third flamer. This means more quality time in combat and less time grinding of materials, especially if you use repair in conjunction with sciencing items.
Repairing with the usage of junk, metal parts, alloys, high quality alloys and metal parts would be more realistic and cool, not the system like it is now.
Just saying.
I don't think using materials would be much of an improvement over the current system. Think about it, would you rather 1) Craft ten guns in a single batch and use the current repair to delay when you'd have to craft the next batch, or 2) Craft a single gun and have to stop over and over again to feed it materials.
With the current system, PvE farming benefits because you can repair weapons on the fly, with whatever you find in the encounter. You can fuse a bunch of damaged grease guns into a few higher % grease guns and be on your merry way.
Now with the material-feed system, your carry weight would get bogged down, and you'd have to leave the combat area to go on a materials hunt. One more negative of just being able to "buy" your weapon percentages back is that players would have to visit the workbenches less. In this scenario, it's not difficult to imagine that the devs will see repair as a circumvention of the crafting cooldown timer and would then seek to place a cooldown on the repair skill itself.
