Right now, I'm deperately clinging to the belief that the Superboy-Prime we saw in "DC Comics Presents #87" is still "somewhere" in a cosmic vortex, and the one who appeared in "Crisis on Infinite Earths #10" and "Infinite Crisis" was a temporal clone (like the Batch SW6 Legionnaires) inserted as a "mole" by the Time Trapper. At least, that's how I'm dealing with "Infinite Crisis Denial"...
In his "DC Comics Presents" debut, Superboy-Prime was definitely a Kal-El, but his Krypton-Prime was slightly different, more modeled after the movie version than the Earth-1 and Earth-2 versions. Also, he was sent to Earth-Prime via transportation beam in the middle of intense red solar flare activity right before the sun went supernova and engulfed Krypton-Prime. So some of Superboy-Prime's "quirks" might be explained to minute genetic variations in Earth-Prime Kryptonians, a slight "scrambling" of genes in that transporter beam, or the cosmic side-effects of the Crisis. Personally, I considered Superboy-Prime "in-between" the Pre-Crisis Earth-1 and Post-Crisis Byrne Supermen -- having power levels closer to the earlier version, but with the Man of Steel's "storage battery" that could keep Superboy-Prime going under red sun conditions.
There's also another overlooked ability apparently possessed by inhabitants of Earth-Prime. Recall that in an earlier Crisis involving Earth-Prime's DC Comics staffers Cary Bates and Elliot S! Maggin, it was discovered that these writers could actually manipulate Reality on Earth-1 and Earth-2! Perhaps sufficient Imagination (or awareness of "The Fourth Wall") was necessary to accomplish this feat -- Ultraa never did anything like this after moving to Earth-1 -- but Superboy-Prime read comic books, and he also has super-willpower. So when he saw images he didn't like in those crystals, Superboy-Prime literally "banged the television set" until the reception cleared to his liking. That's why Lois felt Superboy-Prime's blows, and not Kal-L's when he broke through, and why the Earth-2 Kal-L did not change Reality when doing so.
But Superboy-Prime's biography in "Infinite Crisis Secret Files" says that he arrived on Earth-Prime in a ROCKET SHIP and was raised on the Kent FARM. Huh? Obviously since Superboy-Prime never learned about his true history, he assumed it was like the Supermen he read about. There HAD to be a rocket ship and a farm! And so there was -- Superboy-Prime inadvertantly changed his own past, based on lack of information and romantic boyish dreamings (he claims that his superpowers kicked in right after Laurie Lemon kissed him, somewhat like a Warner Brothers cartoon character going off like a skyrocket after a smooch). So the monster in "Infinite Crisis" was no longer the same kid seen in "DC Comics Presents #87" -- he was literally a "self-made Superman". And who knows what this tampering with his own identity meant for his mental stability?
As for the basic "goodness of the El Family", I hold that everyone should be equally capable of good or evil. It is his struggle to remain good at all times and uphold the values taught by his adoptive parents (despite the corrupting temptations of absolute power) that make Superman interesting, not because he's inherently incorruptible due to some family genetics. And we've seen other examples of "Els gone wrong" in Imaginary Stories and Pre-Crisis Earth-3. Knowing that it's only Superman's self-restraint and love of humanity that keeps him from abusing his incredible powers is part of the Superman mystique that draws admiration and respect among his fellow citizens. If the El Family is basically "good", it's because of their belief system and upbringing, not due to their genetic heritage. And "Infinite Crisis" might show what happens when an El grows up without such mentoring -- old Kal-L was shown as a complete failure as a "father figure", and the results were catastrophic.
"To educate a man in mind and not in morals is to educate a menace to society." Theodore Roosevelt