If you raise a Pokemon from a lower level on PMD, It will usually have bigger stats than a Pokemon that is recruited at like Lv40. Riolu was your starter, which meant it has had more training, Shaymin has just joined and has had no training, and those stats are just the stats at Level 1, usually baby Pokemon have higher stats at that level, but you'll find if you raise a Level 1 Riolu and a Level 1 Lucario all the way to 100 you'll find Lucario with higher stats.
Base stats from the main series games play no part in this game.