I didn't put a whole lot of thought into it, but I can try. I just caught on when you said that one answer is the Poe Sisters and the other answer is very similar.
A parallel of a parallel world, we are. - Something to do with them being spirits, maybe? In darkness we both like to reign. - They're both in dark areas. Although our forms are different, - The Poe and Cubus Sisters don't look the same. Our motive remains the same. - They both try to kill Link.
The bonds we have are critical - They're sisters. And we strengthen them together. The older of us reside in seclusion, and the younger in confusing weather.
That's all I've got, it's been a while since I've played OoT, and I haven't actually played PH yet, I just know of the Cubus sisters.
I don't have a riddle, and I'm not going to have time to think up of one within the next couple days, so I'll let Pinxed do it since (s)he technically got the first part of the answer. --- Current favourite band: Blind Melon
Yeah! Okay, so the floor's open, but anyways, here's what I was thinking.
A parallel of a parallel world, we are. - They're parallels of each other, at least functionally speaking, and they're also in parallel timelines (MM is in child timeline, PH is in adult timeline) In darkness we both like to reign. - They're both in dark areas. Although our forms are different, - The Poe Sisters are ghosts, the Cubus Sisters are little girls. Our motive remains the same. - They both try to kill Link.
The bonds we have are critical - They're sisters. And we strengthen them together. - You need all four poe sisters to advance through the forest temple, and you need all four cubus sisters to progress through the ghost ship. Their "strength" gets stronger as they add numbers to their ranks, per se.
The older of us reside in seclusion, - forest temple is a secluded, broken down mansion and the younger in confusing weather. - the ghost ship goes through a bunch of fog that Link has to take a specific route through, or else he gets "lost". --- The Ancient Cistern: Yo dawg, we heard you like temples, so we put a shadow temple in your water temple, that way you can explore while you explore.