Many Pokemon fans are baffled by these strange two Pichu. Who are they, what is their significance in Pokemon HeartGold and SoulSilver versions, and how does Spiky-Eared Pichu appear in the ancient past in Arceus and the Jewel of Life yet in current-day Ilex forrest in the new Johto games. You can finally know the truth.
Spiky-Eared Pichu (a girl) appears outside of Celebi's shrine only if you have traded the event Pikachu-Colored Pichu (a boy) (a.k.a. Shiny Pichu) from Pokemon Diamond, Pearl, or Platinum to HGSS. It appears as if they are already friends. Well the Spiky-Eared one can't be traded to any other game, because he is like a completely new Pokemon. Actually, Professor Elm explains that his ear has been messed up as a result of time traveling with Celebi (which explains why you found him where you did). It is still unknown whether the other Pichu became shiny as a result of time travel though (he only appears in the present time). But if he was, that could explain the mystery of the rare shiny Pokemon. It would always be a result of too much time travel.
A Pichu duo is not really that new of an idea though. The Pichu bros. were the first, and after this, another Pichu will become popular in the next Pokemon Ranger game... See more about that here!