Emulator

Yes I've used that setting, I previously thought though I got the hangup issue without SuDTR. I now played the game for 90 minutes or so without SuDTR and have indeed not encountered the sound hangup, however the FPS drops I experience without SuDTR are outright extreme, at times the FPS goes under 10 and sometimes takes more than 10 seconds to recover, which doesn't even begin to happen with SuDTR turned on.
So, whether I turn it on or off is just trading one serious problem for another.

The log flooding does however appear with all settings, I tested it again just to be sure, so there might be some relation to that issue behind that.

Speed up disc transfer rate isn't supposed to be compatible with all games, so it's not surprising that something like this happens. One possibility is making fast disc speed eight times as fast as the regular disc speed (or something like that). We had that in the past, but then it was replaced with an infinite speed... I assume it was so that it could be used as a workaround for that old RS2 FIFO problem. Fixing the MP3 performance issue properly like I talked about in https://forums.dolphin-emu.org/Thread-wii-metroid-prime-trilogy--26043?pid=356629#pid356629 would obviously be better, but depending on how long that takes, maybe changing the speed of the speed up disc transfer rate option is a good idea in the meantime? I don't know if it will fix the problems described here, but it has a good chance to do so, and it's very unlikely to make it worse. It's a bit hacky, but it's not more hacky than it already is.

I confirmed this on speedup-disc-transfer rate. Thing is, There's a valid issue with regular disc speeds. I don't really want to close this for fear of forgetting that something is up. I'll ask this: Can you figure out what build began causing the really odd fps/vps desyncs when loading rooms?

It'll take some time but I'll try them through and see if I can zoom in on the build which is responsible. As soon as I have something I'll post it.

Okay, after some 2 hours of testing or so, here is what I found out:
5357 very strong FPS/VPS desync
5308 very strong FPS/VPS desync
5168 very strong FPS/VPS desync
4907 very strong FPS/VPS desync
4898 very strong FPS/VPS desync
4894 weaker FPS/VPS desync
4889 weaker FPS/VPS desync
4887 weaker FPS/VPS desync
4875 weaker FPS/VPS desync
4849 weaker FPS/VPS desync
4800 ES_LAUNCH error
4724 ES_LAUNCH error
4601 Less drastic slowdown, weaker FPS/VPS desync
4555 general strong slowdown, weaker FPS/VPS desync
4523 general strong slowdown, weaker FPS/VPS desync
4494 general strong slowdown, weaker FPS/VPS desync

So to conclude:
-SuDTR does help with evening out the terrible load times throughout all revisions, this is especially noticeable when opening the doors to really big or open rooms, where the game will freeze for 1 or 2 seconds without SuDTR turned on
-The mentioned FPS/VPS desync which seems most easy to be noticed right when the game starts in a save station seems to have been introduced with 4898
(I'm not sure the revisions 4897/4896/4895 exist as they don't appear in the download lists)

It's from the more accurate Disc Timings. Goddamn it. THere's something we're missing or something's wrong, is it what that guy that seems to know everything about the GameCube/Wii said, or could it be even more?

Wait, so this isn't just a performance problem, it's something weirder? Why would FPS and VPS be desynced?

If you want to test if the VolumeWiiCrypted problem is what kills performance, PR 1969 is ready for testing: http://dl.dolphin-emu.org/prs/pr-1969-dolphin-latest-x64.7z

Also, I must ask... SuDTR didn't change anything when using 4.0-4894 or older, right?

SuDTR DOES change the performance in earlier versions as well. I'll try to make it clear.
In version 4898 or newer there is a drastic desync which SuDTR fixes mostly. Without SuDTR the desync when loading in a savestation in Elysia is as drastic as 6 FPS to 50 VPS. If SuDTR is turned on then the worst desync I get is 30 FPS to 50 VPS, which is hardly noticeable.
In version 4894 or older there still is a slight desync, though it only goes down to 30 FPS to 50 VPS, like mentioned above, here however SuDTR on or off makes no further difference.

However there is the desync on the one side, and many severe slowdowns all throughout the game on the other side.
These severe slowdowns as far as I perceived it exist throughout ALL the revisions I tested, and throughout ALL of them SuDTR helps drastically, at the cost of potentially causing the mentioned hangups.

So SuDTR fixes two things, the desync (at least somewhat) and it also vastly improves the general performance. As I said, playing MP3 for an hour without SuDTR was a real pain. To make a comparison, with SuDTR there are no drastic slowdowns, unless a room is simply too complex, but even then it rarely goes below 40.
If I have SuDTR turned off it's like walking in syrup for half the game. These slowdowns do not happen with SuDTR turned on, whatever revision I use it's the same.

I also tested the latest revision, it seems to change nothing.

That you say "SuDTR on or off makes no further difference" does make it sound like it doesn't have any effect on old versions... For Wii games, those versions should act roughly as if SuDTR is on (except for the game-breaking problems?), even if it actually is off.

PR 1969 hasn't been merged yet, so you won't be able to test it if you're using the latest revision. It would be useful if you tested it using the download link I posted earlier. Also, I realized this morning that PR 1854 would be useful to test too: http://dl.dolphin-emu.org/prs/pr-1854-dolphin-latest-x64.7z

JosJuice: If the game can't load fast enough, as I learned in EXI changes, the FPS will drop but the VPS will remain full speed. I think your more accurate disc timings may be too slow for this particular game.

Actually, the reason I suggested PR 1854 is that I suspect that the DI commands are taking so long time that they are blocking other WII_IPC_HLE commands from being executed. The PR changes this so that DI commands don't block other commands at all, by bypassing the WII_IPC_HLE scheduler. I don't think that the disc speed itself being too slow is the problem, because the Metroid Prime games just prevent doors from being opened when data is being read, they don't make everything lag. However, that the problem is that WII_IPC_HLE commands are being blocked is just a guess from my side, so maybe PR 1854 won't help at all...

Let me cc MaJoR, our resident Metroid Prime expert.

"PR 1969 hasn't been merged yet, so you won't be able to test it if you're using the latest revision."
Ah, sorry, I meant I tried that link as well as the newest revisions, just didn't write it properly. PR 1969 didn't help.
SuDTR did improve the performance of all master versions so far. It's only that with the recent ones it also helps with the desync.

So if I got that right then the expected behavior is that the game should run pretty much the same with or without SuDTR, which it currently does with NO revision of the master branch, right?

That's what I get with PR 1854, I think your guess might be spot on! Trying this one is a really drastic performance improvement over all other version I tried, and the desync is also gone.
And finally I do see what you all seemed to be hoping to see, SuDTR does not make any real performance difference anymore. After a bunch of test runs from the Save Station A in Elysia to the Spire Dock I got no real lagspikes, and in most of those test runs the game worked even perfectly, apart from a tiny surefire lagspike when doors open, but that's barely noticeable if you don't pay close attention to it.
The only difference SuDTR now makes is that the doors open instantly, but you know, they didn't do that in the Wii version either. It'd be cool to make that possible without inducing other bugs, but that's not really the point here, nor is it any important.

So yeah, PR 1854 seems to be fixing the issue.

Glad to hear that, I tried my best to supply as much detail as possible.
And well, as I said above the log is always being flooded with these [IPC_HLE\WII_IPC_HLE.cpp:370 W[WII_IPC_HLE]: Trying to open /dev/net/kd/request as 13] messages when playing MP3, so I guess that also was related to this.

On my way of playing Metroid Prime 3 I might find and post more bugs some time [already saw a few weird but much less dramatic bugs], but first I'll wait for this fix to end up in the master branch and then I see if I find anything else.

Also the help was really fast and nice, dolphin and you guys are awesome :)

Fixed by 4.0-5531. https://dolphin-emu.org/download/dev/8cc6e5cff9cff74483c3cc939f1bc7c934570549/

Haha, awesome. Can't wait to get back to playing and testing :)