A better method to determine cost would be to have (item level x damage percentage = cost), this way you are only paying for what is damaged.NPC repairs: these should stress convenience in order to get players to use them over player repairs.
NPC repairs items to 100%
Rank 1-20 repairs cost a flat fee of 1,000 gil
Rank 20-40 repairs cost a flat fee of 8,000 gil
Rank 41-50 repairs cost a flat fee of 10,000 gil
NPC repairs jewelry too
"Repair all equipped items" option gives you a 20% discount on total repair bill
Any rank 20+ item repaired by the NPC that is at 85% durability or above costs only 3,000 gil to repair.
Add a repair NPC at every Aetheryte Camp.
Agree that NPC's should repair to 100% and accessories should be included.
Teleportation
Remove Anima completely
Remove the option for players to teleport via the menu.
Allow players to select an Aerthyte and teleport between nodes for a charge in Gil, (the further you teleport the more it costs the player)
Alternatively you could add teleport NPC's similar to how FF11 did outpost warping.
Fatigue
I have recently been playing Allods online and they have a fatigue system also but a player can pay the Inn keeper money to regain the built up fatigue. (its actually a bonus system)
Although I think you are planning to remove the fatigue system if you did a similar system to allods you could keep the fatigue system and also make an extra gil sink.
** A player would only be able to build up a certain amount of fatigue each day**
** Cost increases with each rank**
FFXIV has Inn keepers but they serve no purpose so this could be a nice addition.