I would need to go through and battle them all to give you specifics but a large portion of NPCs only give you $1-3k and they just aren't worth fighting. Considering how dynamic the markets are (Everstones, Mushrooms, Heart Scales etc.) I feel we need a stable way to earn money, that isn't constantly changing. The reason behind the NPC nerf was the addition of Unova, which gave us more NPCs to fight, but wouldn't it be better to balance that by making them more difficult? The gym rematches are somewhat difficult with fair payouts and it's the most reliable way of earning money right now. I don't see the harm in increasing the difficulty and the payouts of other NPCs.
Increased difficulty + increased payout (maybe longer cooldown?) > completely nerfing NPCs.