This is just a supposition, but hear me out:
Within several locales of the region you would be able to find certain barred-off places that have no apparent means of access. There might be one inside the volcano, one situated deep in the jungle, and still another leading into the edge of a quarry. All in all, there are eight such areas, but you'll know they're connected since not only will they bear the same suspicious insignia on the door that blockades them, but also pressing A by the doors will tell you that it "sealed fast with an ancient lock".
But get this! After you defeat the Elite Four about three-four times, the gyms will toughen themselves up to extraordinary proportions, pushing into the 80s in terms of levels while your projected mean team level after beating the E4 lies in the 60-70 range (you need to use Pokemon caught/hatched in your version for this, otherwise the game will state that the trainer-Pokemon bond is too weak). Each one of the gym leaders will give your badge an Activation Ceremony when you defeat him or her for the second time around, and with each ceremony you gain access to one of these areas. You need to find which area this is - you can tell since its insignia will glow - and just go up and press A, and presto! it will open.
What exactly do these areas do, might you ask? Well, normally they don't seem all that special - all that stands out about them is that they are all the same uniform size, rather spacious, and they contain a large Pokeball insignia on the floor - but beyond that they simply contain the local stock of Pokemon. However, once you open all of them up and defeat that level 90-100 Elite Four, something miraculous! you awaken the spirits - all of the Pokeball insignia light up in the room, and when you return to them all the battles have a really scary-creepy remix to them as you fight souped-up, fully evolved, generally good-IV possessing, EV trained level 100 wild Pokemon that contain incredibly rare egg moves in these places. You can't catch them via normal means, either - in fact, you won't be able to catch them until two-three years in the future, since you since the Emerald equivalent version to obtain a Feral Ball. They're very pricy at $30000 a piece and function only to the extent of a Great Ball on these Pokemon, but it's well worth the blood and sweat to get a truly valuable and reliable Pokemon from these places.
Of course, you still get a boatload of EXP points from them, so consider yourself satisfied.
