Sorry for the delayed replies. I've been quiet lately because I've been busy working on things.
In all honesty, the updates taking longer than I expected due to unforeseen changes made by the devkitPro team. For example, they recently abandoned the threading system that's worked perfectly fine in homebrew apps for decades and replaced it with something called Tuxedo. However, Tuxedo doesn't support time slicing, which means you now have to fine-tune thread priorities and manually yield to avoid race conditions where one thread can block another.
Why this was forced onto every developer instead of offering both options, I don't know, but I really don't like it.
with the next cIOS will the EmuNAND again have to be recreated? or was that only the case with that particular revision/update of USBLoaderGX?
No. That was only an issue with older versions of the loader, because it failed to install shared content correctly but still updated content.map as if it had been installed. As a result, some games wouldn't work because files were missing.
a weird thing people rarely mention is that problematic games like Majora's Mask and Paper Mario did work if you waited long enough.. at least that was my experience going back two years now.
This is with d2x-v11-beta3 and USB Loader GX r1283.
If you reset the loader to it's default settings or create a new EmuNAND and you still experience problems, then there's a good chance my next update will fix things for you.
The second reason for my post is my curiosity regarding whether it's possible to do 2 things with VC games.
1. Patch on the fly custom palette (NES)
2. Change button mappings. I use mostly gamecube base layout controllers and some snes games have inconvenient setup (for example Super Mario World).
I won't make any promises, but these features might show up in a future release.
I use usb loader gx for playing wii games from SD card, 0 problems so far. But I'm wondering if Wiiflow is still better for sd card users?
Wiiflow is better, period!
Haha, I admire the confidence

But in all seriousness, they both use the SD card in exactly the same way, so neither is really "better" there.
WiiFlow focuses more on UI customisation and plugins, whereas with USB Loader GX I've focused more on game compatibility and adding new features. So which one is better is subjective, since it'll depend on your needs and what appearance you prefer.
USB Loader GX has received a number of updates addressing long-standing game issues while also adding new features. And although some of these improvements have made their way into other loaders over time (e.g., WiiFlow 5.6.0), USB Loader GX still tends to offer broader compatibility and more features. For example, it supports game backup creation, correctly pillarboxes 4:3 games on vWii, and for the past 9 months you've been able to pair Wiimotes directly within the loader.
My next update is a major one that'll improve both game and drive compatibility, among other things. However, I'm taking a "when it's ready" approach with this update, so I can't say exactly when it'll be released.