Mysterious Treasures is based on the Sinnohlegendary trio, Uxie, Mesprit and Azelf, hence the Japanese name The Lakes' Secret as these Pokémon reside at the bottom of Sinnoh's lakes.
Like EX Sandstorm (which was also the second expansion for its particular generation (III)), Mysterious Treasures introduces the two Fossil Pokémon introduced in Generation IV in card form. The new rule regarding Fossil cards first announced with the release of Diamond & Pearl applies to the new Skull and Armor Fossil cards released in this set.
Mysterious Treasures also introduces Pokémon that come with held items; in this case Berries. These held items work in the same fashion as Poké-Bodies, in that the effect the item provides is active whenever the Pokémon is in play. This is another game mechanic derived from the games, in that some wild Pokémon are holding an item when they are caught.
Mysterious Treasures features the secret card Time-Space Distortion, which was previously only available as a Japanese promotional card at Battle Road Spring 2007. Like its Japanese counterpart it features a holographic border, making this the first English Trainer card to have this treatment. It is also the first secret card included in a set since EX Holon Phantoms.
Although there are cards for Abra and Alakazam, there is no Kadabra; one of Abra's attacks allows it to evolve straight to Alakazam. The noticeable exclusion of Kadabra is likely a result of the Uri Geller controversy.