The end of the story is not the end of PokéPark 2. New areas open up, about forty Pokémon become available, and the Legendary Pokémon of Unova enter the scene. Here is what awaits you, based on Poképédia.

The Lakeshore.
The Lakeshore.
The Light Machine.

The Mystic Area

Timburr repairs the broken bridge in the Verdant Garden: it leads to the Lakeshore, a peaceful place inhabited by Water- and Grass-type Pokémon. There you will find the altar of Landorus on a small island, and the portal to Reshiram up on the heights. In the Verdant Garden, Dugtrio also digs a tunnel to its hideout.

Timburr.
Landorus.

The Forces of Nature and Zekrom

Tornadus waits on Surf Beach: beat it in a race. It brings along Thundurus, at the Colosseum, which also has to be beaten in a race, and then Landorus, to be faced in a duel at the Lakeshore. Thanks to the three of them, Reuniclus opens the Black Ideal Sphere in its laboratory, using an oven-like machine: it leads to Zekrom, via the stone at the top of the stairs of the Wish Palace.

Tornadus.
Thundurus.

Reshiram and Darkrai’s return

The Lakeshore portal to Reshiram requires 20 White Truth Feathers, which are found in the Wish Park. Once Reshiram and Zekrom have been called upon, Darkrai is saved from the Vortex of Darkness and takes its place in the palace again. Gothita, Gothorita and Gothitelle can then be challenged.

Darkrai.
Gothita.

Other challenges

  • The Colosseum’s Grand Tournament: about ten series of battles, with no healing, and two assistants who can each be summoned once. It is optional and gives no special reward.
  • The Wish Park bosses, to be replayed in order to befriend them.
  • Samurott and Emboar, to be beaten in a duel.
  • Wailord, on the beach, in exchange for 50 Honey Pots; Lucario at the Colosseum; Emolga, Staryu and Kecleon, who keeps the player’s stats.
  • The photo of Munna for Duosion: give it Scent Candles at the Colosseum so that it moves around, wait without touching the controller until your Pokémon falls asleep as Munna passes by, then take the photo without switching to first-person view.
Samurott.
Emboar.

The full list is on our Pokémon pages, by area: Cove, Arbor, Crag, Factory, Mystic and Wish Park.