I think it is somewhat understandable, at least on the no faction wars front. The journal, from what I recall, covers the time right after Hearth's Warming, so everypony alive can recall how they were almost all wiped out, because they couldn't stop the factional infighting. On top of that, I can see them recognizing that the old wounds are still too close to the surface for any one type of pony to be accepted as rulers for the others, and if they split up again, that would run the risk of the Windegoes eventually returning. The existence of the alicorns solved that problem, as they weren't actually part of all the prior infighting. That they look like a combination of the three main types of ponies is just a bonus. When there's a choice of "fight amongst yourselves and freeze to death, or play nice and live", I doubt too many ponies were eager to try to press any claims.
That said, I will agree with you on some of the other bits of silliness, like the way the potential war with the Griffons was stopped. Then again, griffons probably aren't natural farmers, so the point of the invasion might have been to capture the Earth Ponies to farm for them. And then Luna set up a [strike]tribute[/strike] trade deal where the ponies would provide luxury baked goods and the like, removing the need for the war.
Back on the subject of genetics, may I ask how are you doing the pony subraces? (Specifically, how the game decides what type of pony is born.)
