I think it's going in the right direction, but I agree that there isn't quite enough money being made. I have a full team of pokemon just under level 50, and in that grind I have earned enough for the pokeballs to catch a few other pokemon (5 or 6 more in my pc) and a house now, If I wanted it. I'm not a fan of the mining idea. We would need to create a new wilds map like on the non-pixelmon server.
Instead, I would like to see more ways to supplement the economy without a totally new concept like mining. A slight pricing change would be nice in the pokemarts. Adjusting some signs so that not everything is 5 for 1 nugget except enderpearls. Keep the common ones such as leather and raw beef, but bump some of the more rare ones up to 4 or 3 for a nugget. For example, magnemite/magneton is quite rare. They drop iron, and I've only ever found 4 of it. It doesn't make sense to have that iron valued at the same price as something as common as leather. Adding new drops to pokemon without them would help too.
I would also like to see things such as small amounts of money won from npcs, or the chance to pull up a nugget while fishing, but I'm not sure how plausible these are.