a flawlessly wise ruler
Nah, she's damn good, but not flawless. We've even seen her get thrown off her groove a couple times, and presumably the whole Nightmare Moon bit could have been nipped in the bud if she was a bit more on the ball way back when.
To quote one of my favorite fanworks, "I am very old, and I have made many, many mistakes. That is what some creatures call wisdom."
* It was actually Luna, but you get the idea.
Not to mention, you know,
engineering the cause of immense amounts of property damage and scaring the bejeezus out of her own retinue because she was bored. Even if it was awesome.
Regarding "castes", Rarity's apparent class anxiety kind of hurts that theory. Sure, she's classier than most Ponyvillians (is that a word?), but she's that way by choice, it doesn't look to be something she was born into. Notice how she also seems to idolise Canterlot in spite of clearly not living there herself.
I'd imagine living with her parents for any length of time would inspire a certain amount of anxiety about class and presentation. Shit, if I grew up in that house I'd probably be George Zimmer or something.
Also, if unicorns were some kind of ruling caste that would make Snips and Snails the next generation of high pony society.
And it might
still beat the last one :|
Don't blame science for Twilight's shit methodology.
And honestly, don't blame science for not being able to trump Pinkie. I swear the girl's an eldritch beast in disguise.