The fastest way to get money is Le Wow. But, it does cost 100K to attempt. I built a strategy to do it.
First, you need 2 high level Pokemon (70 or higher), preferably ones who can use moves like earthquake or surf ( I use Charizard and Flygon). Make sure they also have a stalling move (Like fly or a stat raiser) so you can be more precise with the turns completing.
Secondly, you need an amulet coin (for increased money earning) and prize money O-Power (level 3 preferably) or a friend who can use it.
Now, have your two high levels in slot 1 and 2 of your party. Make sure one has the amulet coin. Walk into Le Wow and use the Prize Money O-Power. Then talk to the lady. Choose the double battle and pay her 100K (Can be lowered, not sure how). Now, you go through a series double battles. Each double battle gives prize money ( and good EXP for leveling Pokemon). Try to win the battles in the target time stated for more end money. Once all of the battles are over, you are rewarded Balm Mushrooms, which go for 6K each. If you get all of the battles in the correct amount of turns ( and none of your Pokemon fainting), you get 25 Balm Mushrooms.
25 * 6000 = 150000 Poke, which is more than you had to pay to enter. Also, you get 10K for the first 2 battles (Without Amulet Coin) and 4K for the last 3 battles (Without Amulet Coin).
150000 + (20000 * 2) + (8000 * 3) = 24000 + 40000 + 150000 = 214000 Poke per run. That did not include the Prize Money O-Power, but it did include the Amulet Coin.
214000 - 100000 (Fee to enter) = 114000 Poke profited per run, if everything goes right.
If you do not have 100K Poke to enter Le Wow, you can do Elite Four runs. With Amulet Coin + Prize Money O-Power and/or the Battle Chateau to earn 100K easily. Also, if you are lucky, the people you beat at the Battle Chateau might give you selling items, like pearls and nuggets.
Both the Elite Four and Le Wow give lots of profits, but Le Wow is much easier seeing that your opponents only have 2 Pokemon in double battles (3 in triple and rotation), and are always level 63. Also, unlike the Elite Four, the people in Le Wow do not use full restores.
EDIT: With the new Event Inkay (with a move called Happy Hour) you can make EVEN more money. But, as of now, it is a Japanese only event. The move increases the money earned from battles.
EDIT: If you throw in PayDay, you can get EVEN more money. PayDay takes the level of the user, multiplies it by 5 (in gen 3 or higher) and scatters coins of those value. AND, it is effected by Amulet Coin (Pokebank will allow you to move a Meowth/Persian up to X and Y). And then at the end of the battle, you pick the money and it is added to your amount.
EDIT: If you complete the Le Wow challenge perfectly at least once, the cost for it lowers.
EDIT: If you use Amulet Coin + Prize Money O-Power 3, and have the discount, you earn a total of 150000 + (60000 * 2) + (24000 * 3) - 90000 = 252000 per run, plus lots of EXP.
Best Answer
The new limit is 9,999,999 pokedollars, which i found out by having too much free time and over using the prize money o-power. The mega stone prices go down because of how famous you are in lumiose i believe, which is increased by your first league victory...i have seen prices for them go down to 150,000...either this is lumiose fame or they used a lvl 3 o-power, im not certain.