I've managed to collect (what I assume are) 3 of those keys already. I guess this would be a spoiler, though we've been bandying plenty of those about.
After I got the dark visor, I started using it everywhere, and I saw this creature outline underwater. I couldn't interact with it at all, but later in Dark Aether in some other area, I saw the same shape, only filled out. I went hopping across the purple stuff to it and shot it. That brought it out of stealth or phased mode (or whatever) and I killed it with one light-beam shot. It left a key to the sky temple. Later I hopped across some normally invisible platforms for another, and got the third a while after that.
I fought and beat Dark Samus 2 with little trouble. Didn't even read strategies on that fight. Then the game threw me a nasty curve with a bot inside a big cylinder filled with spider-ball tracks. I was not ready for a boss fight. I wasn't even all that healthy when I got locked in there with him. I didn't know what to do, so that was that. 2nd attempt went much better, and got him out of the way.
I was hopping around some complex and even spinning ball tracks in a big outside area when the sandman found me. Enough for one day.
Ooh, cool new suit of armor. It looks so different from anything else I've seen Samus wear (including the skimpy prurient outfits).
OK, I'm rounding third and heading for home. I took on this enormous 4-legged robot a couple of nights ago. I almost had it beat, but then I couldn't quite make the last couple of moves needed to bring him down. Dark Aether's constant damage took me out more than he did, after more than a few failed attempts. So I went on to do lots of exploration and found 4 (four!) energy tanks, bringing the total to 13. Found other goodies too, mostly missile expansions, a few power-bomb expansions and a couple of Sky Temple keys. Last night, I went straight to Round 2 with the big guy. This time, it was almost easy. I managed to keep at full health until the tricky part, and I got through that with only a couple of missteps. I got the last missing weapon from him, and returning the temple's energy got me the suit I mentioned.
I went on to find the high-power attack for that last beam as well as the last energy tank. Then I went after a few more Sky Temple keys I had already figured out, but couldn't get to because of Dark Aether hazards I couldn't get past. The new suit fixed that. I returned the keys in my possession to the access point, and found out which I was missing (only 3). You know, Que, I sort of like this quest. It's the kind of thing I like to do in Metroid games, much much more than fighting hard bosses. (I should note that I have only used a walkthrough on bosses, and not even all of them. I've been very careful not to spoil anything else.) It wraps right into the familiar task of scanning everything.
If you get all your Luminoth keybearer and temple-access room scans, the clues will nearly pinpoint where you have to go. There are 2 clues per key, one from the room's key slot and one from the log of the dead keybearer. The keys are always in the dark world, while the bodies of the keybearers are in the corresponding part of the light world. I went on to find 2 of the 3 missing keys. The one that's left I already knew where it was, because I saw the outline of the creature holding it (with the dark visor). I just have not figured out how to get to it in the corresponding Dark Aether area.
So this is where I quit last night.
I'm glad I decided to stick to the game after my ranting. You're right about it being rewarding. A lot of thought and love went into it. It would have been a shame if I allowed some unfortunate excessive difficulty here and there to scare me away.