The Mother creates her children so that they can fulfill her wish. When they fail to do so after some time, she kills them. Why doesn't she simply wait until her children advance technologically enough to be able to send her home? Because she knows they might turn against her first. If you take a look at the previous generations of children, none of them prioritized fulfilling Mother's wish. Some had other goals on mind, some decided that the task given to them was impossible - and some did not even know her, which was a result of deliberate scheming of the previous generation. The Mother didn't fail to create children that would be able to fulfill her wish - she failed to create children that would be willing to do so.
A few things occurred to me about La-Mulana last night. Firstly, the traps weren't put there by anyone. They're the Mother's immune system. And notice that the place is, well, ruins? This is why you have to kill the Mother: her body has degenerated to the point that even if she were sent into the sky, she would be unable to function, and she is in extreme pain. Furthermore, the front and back areas are a large part of a theme of opposites. The tutorial level Guidance Gate and the aptly-named Confusion Gate. The Mausoleum of the Giants, recording and honoring each member of the dead race and filled with statues of how they looked while alive, stands in contrast to the Graveyard of the Giants, showing the cold reality that no matter who you were when alive, you are little more than a lump of organic materials once you die. There is, of course, the male Temple of the Sun and the female Temple of Moonlight, and the Chambers of Extinction and Birth. But this runs deeper, as the Mother has an opposite as well: you. She is Birth, and you are Death. She created races to let her get home, and you are a member of the race that never knew her wish. She is the idealistic hope that she can go home, and you are the grim reality that this is impossible.
Actually if you look at the ruins' maps you'll notice various layouts that vaguely resemble something like a flower, or a snake, or a key, or a ring, or a dolphin... And then there's the Shrine of the Mother, which bears a resemblance to a human body. It's not that the ruins are her body, the ruins are there to protect her body from being reached, whether these were her children's intent or not.
Shorn put a LOT of effort into making sure Lemeza would be the one chosen by the philosophers. How much effort, you may ask? He made it all the way to the core of the ruins, which means he solved every single puzzle there was to solve...and then put them all back in place for Lemeza to prove his worth! He had to have solved them, or his final message on his laptop wouldn't be in the chamber of the Mother, and it is even possible that the 'unsolveable puzzle' that was left in the Twin Labrynth was MADE SOLVABLE BY HIM, just so that Lemeza could beat it too. Before you praise him for being father-of-the-year, remember he was also waiting there so he could snatch the treasure after Lemeza retrieved it from the ruins. He did all of this just so he could outdo his son in the end.
In the remake, there may be a reason that Shorn steals the treasure at the end; Lemeza steals the Feather item earlier, and Xelpud tells him he will pay one day. In a sense, then, the ending of the game is Laser-Guided Karma for Lemeza.
The problem with that theory is that Shorn says he wasn't chosen by the philosophers, and the way to the Mother's room is only accessible through a philosopher creating a ladder, though maybe his dad isn't bound by video game laws and could have simply jumped down. But even if Shorn could reset all the traps I don't think he could resurrect all the bosses, and the only way to ultimately get to the Shrine of the Mother is by opening the pathways by killing the bosses. My theory is that Shorn is simply following the paths you open, letting you do all the hard work so he can benefit off it. I mean, that's what he does in the ending, so why not just let Lemeza fight all the bosses too?
Lumisa in La-Mulana 2 wears an American flag as a bandana, and her jeans have a patch of the American flag but with the 50 stars replaced with the Japanese flag. Why? Because La-Mulana, a Japanese-developed game, is surprisingly popular amongst Americans.
It could also be to reflect her Japanese-American heritage.
Those feathers in Mulbruk's headband sure resemble the Feather item don't they? Sure enough, the special ending after beating Hell Temple reveals she can triple-jump.
A few notes on the bosses' musical themes - specifically the riff they begin with.
Guardians have their own riff. - however, those from the first game have a different riff than those from the second game. This is because they're tasked with protecting a different set of ruins (La-Mulana and Eg-Lana, respectively).
The first game's final boss has two different musical themes. The first uses the same riff as the La-Mulana Guardians, which hintd that it's not the "true" final battle. The second uses the same riff that plays when the player first enters the ruins - fitting, since said boss is the Mother herself, who is the ruins you've been exploring this entire time.
The second game's final boss uses again the "entering La-Mulana" riff. That's because the final boss is a copy of the Mother from the first game.
The means to access Hell Temple is insanely obtuse and convoluted, even by La-Mulana standards, to the point where it feels almost like it was deliberately made to be impossible for anyone to figure out unlike the rest of the puzzles in La-Mulana, which were deliberately made to find someone capable enough to kill the Mother. La-Mulana 2 eventually reveals that Hell Temple is actually the center of Eg-Lana, not La-Mulana. This means the process by which you unlock Hell Temple is so convoluted because you're not supposed to be able to enter it at all, since Eg-Lana is a prison that is not supposed to be accessible to modern humans, and you're effectively glitching your way into creating an entrance to it.
Probably a case of You Didn't Ask on Xelpud's part. Alternatively, Shorn already knew, but was trying to solve it himself bit by bit; he only revealed it to his son once he reached the center and realized he couldn't progress any further himself because he wasn't chosen by the Philosophers.