There are a few fixes/tweaks from Universal Tweaks that would fit pretty well in this mod, @ACGaming has also expressed interest in wanting them in this mod instead so we can have a more streamlined fix mod for Thaumcraft 6. You can find what was done here, the tweaks are likely out of scope for this mod but I'll list them here just in case.

List of fixes:
-Duplication Fixes - I've noticed a few are in this mod already but there may also be a few from Universal Tweaks that are not included yet.
-Firebat Particles - Firebats have missing particles unlike previous versions.
-Flower Bounding Box - Flowers do not have randomized positions like vanilla flowers do and thus end up with a weird hitbox because of it.
-Wisp Particles - The particle from wisps upon hitting them are actually much smaller unlike previous versions.

List of tweaks:
-Focus Effects - Revamps cast sounds of several focus effects (especially the annoying ice one) and adds sounds on impact similar to the air or curse focus effects.
-Focus Mediums - Makes different focus mediums stand out more by playing additional sounds (e.g. the bolt one plays a shock sound).
-Rarity - Primal Crusher has an epic rarity, while the thaumium/void tools have the same rarity as their armor counterparts for consistency.
-Spiderlike Eldritch Crabs - Crabs flip all the way like spiders on death.
-Stable Thaumometer - Makes the thaumometer not constantly bob while scanning with it (I think something like this for the gauntlet would also be nice).

Some fixes/tweaks were also mentioned in a few suggestions:
Disable right-clicking items on boiling crucibles
Make Thaumcraft's Research Table look for ore dictionaried Bookshelf
Several bugs were mentioned here
Thaumcraft Tweaks
ThaumicJEI / Thaumcraft API fixes

Not Universal Tweaks related but I might as well also list these to help keep track:
-Champion Mobs - Another missing feature from 1.12, champion mobs exist in the mod's code but do not spawn naturally.

-Resources - Apparently items like the Primal Crusher and Triple Meat Treat were supposed to have animated textures like older versions but don't for some reason. A missing sound that should be easy to fix was also mentioned quite often. The inlay textures have an odd white border on them that is addressed by this resource pack. Several Thaumonomicon entries in Thaumcraft 6 have a couple of typos, which would be nice to see fixed.

-Runic Shield HUD - While runic shielding is active in 1.7.10, an animated overlay effect would display on your health. This was since replaced with absorption hearts as of 1.8, a (now inactive) mod called Thaumcraft 6 Enhanced does actually attempt to restore this but it does have compatibility issues from what I know.

-Thaumonomicon Font - The Thaumonomicon used the unicode font in earlier Thaumcraft versions. This would be great to have as a config option without needing to have force unicode font on.

-Warp - Warp had an overlay effect when warp events happen in older versions but this does not happen in 1.12. You actually can still see the overlay effect while the Deadly Gaze effect is active so restoring this shouldn't be too difficult.

This is a very thorough list, thanks for making it. I think I want to keep things limited to mostly "real" fixes for the first release so I can actually get it out instead of keeping it in github beta forever, but I guess for simple things like particles I can take a look at those.

There do seem to be a lot of dupe fixes in Universal Tweaks I don't have yet, I'm probably going to work on those first. In general, the things you have in the fixes section seem easy enough that I can add them in the initial release.

I have to properly go through the rest of the list, but a few first thoughts:

1. I think the foci sounds would be a nice addition even if it's not really a "fix", and they shouldn't be too much work to add in
2. I also think the ThaumicJEI research event issue should be fixed, because I added client events for gaining research and knowledge. The only thing I have to check with that is that I'm not breaking other mods, because technically the events will be firing twice now in singleplayer because I subclassed the normal TC event.

Since these fixes/tweaks would also be in Universal Tweaks, we could maybe do something like I do with Thaumic Augmentation now and stop this mod from applying some of the tweaks if Universal Tweaks is detected.

Thanks again for collecting this list, it's very helpful!

@TheCodex6824 Just for your reference ThaumicJEI's author said the event issue is only due to a bug in Thaumcraft's API (Azanor/thaumcraft-api#46)

No problem, I'm happy to help out with pointing out bugs! Will also state that AC is planning to remove any of the fixes/tweaks that make it into this mod because Universal Tweaks is getting quite big with all the features it has, so special compatibility between both mods wouldn't really be necessary.

Status of this stuff so far: everything in the "fixes" section should be in now. I still want to do the tweaks, but before that I'm working on getting at least an alpha out on CurseForge so people can start using it.

I personally recommend marking the file as beta, otherwise it won't be as visible on CurseForge unless that is the intention. :)

(Also @TheCodex6824 keep in mind ACGaming/UniversalTweaks#341 has several bugs mentioned in it, it's not just tweaks)

I personally recommend marking the file as beta, otherwise it won't be as visible on CurseForge unless that is the intention. :)

I could make it a beta instead, but I'm trying to communicate that I cannot guarantee it is 100% modpack-ready or bugfree. Things seem mostly fine in testing so far, but we can't test every combination of addons so something could still be not working.

(Also @TheCodex6824 keep in mind ACGaming/UniversalTweaks#341 has several bugs mentioned in it, it's not just tweaks)

Yeah I meant the "tweaks" section of this issue - a lot of the things in the issue you linked are the same as #4. So far I dealt with the focal manipulator bugs, but I still have to fix things like the potion IDs.

I'm trying to communicate that I cannot guarantee it is 100% modpack-ready or bugfree.

You have high standards, I think no Minecraft mod released was ever 100% bug-free (or even close to that) - I trust it'll be great to integrate Thaumcraft Fix into modpacks and over time with community feedback further polish it.