the reason the mender npc is favored are simple:

1) the need to switch between each DoH for each part concerned.
2) the fact we can't gather anymore the dark matter
3) mender npc are simply easier than player repair.

you want the repair from player more used? simple, put back dark matter in gathering, make it's easier to repair stuff as player by not switching between class, if you have the class at the right level, even in dragoon you must be able to fix this.

why do i put the lack of gathering to the reason? people don't save a lot by doing player repair. actually exept if you use the seal of grand company you save almost nothing.