While I'm sure there's no Biology lesson behind the reason why, it's simply for the sake of Game Balance. Imagine breeding Ditto and Palkia, and getting a lv.1 Palkia from the egg.
You trade this egg from Pearl to Diamond, then start a new game in Pearl. You get to Sandgem Town, and trade your starter for that Palkia. You would have the 3rd most powerful Pokemon in the game at your disposal, and you wouldn't even have a single badge.
The developers couldn't have you running around with legendaries at the beginning of the game, because that'd be WAY too easy. Plus, the storyline makes no sense, in this example:
"Have you heard of the legendary Pokemon that can travel through and manipulate Space? It's said, in a legend, that it created the Universe."
"You mean this little guy? I named him Bob!"
I must admit that it's pretty silly and funny in this perspective. =P
But you can see that even the storyline takes a hit, if you look at it in that sense. If you already have Palkia, then where would the original Palkia come from? What are Team Galactic fighting for, if you already have they needed?
The storyline itself doesn't change, but for people who are huge buffs on storylines, it would disappoint them very much.
I think those are the only two reasons I can think of, but they're major reasons.