Manaphy breeds to create Phione, but Phione does not evolve into Manaphy. So it's clearly different from normal breeding.
Manaphy's total stats are 600 same as Mew, Celebi, Latias, Latios, Jirachi, Deoxys, Cresselia, Shaymin, Victini, Landorus, Meloetta and Genesect. There are also 18 other legendary Pokemon with lower stats than Manaphy.
Maybe you are thinking of Phione? Phione's stats are only 480. It doesn't have a brilliant learnset but it has a few options.