The Magma and Aqua event can be actually done BEFORE Shelly. There's also a new event after Shelly, involving the battle between you and the leader of the opposing gang, which you get Carvanha (if in Aqua) or Houndour (if in Magma). I've also seen a Houndour in the abandoned Magma Gang base if you're in Aqua.
Also, once you get Rock Smash, you can access the dark cave in Beryl Ward/Beryl Cemetery, and on Windy days, you can find a Nuzleaf Gang with a Level 50 Shiftry. After you beat them, you can take FIVE Nuzleafs. On Sunny days, after doing this Event, a Tropius will be there.
Also, if you don't get the Dull Key before beating Shade (and after beating Shelly), you can't get it until you beat Aya and can use Strength.