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Forge Mod Loader has found ID mismatches
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ID 21420 from Mod ThaumicTinkerer is missing
ID 21419 is mismatched between world and game


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enchanting bottle for the magical fabric

First, some background on firsthand experience with TC3 and secondhand knowledge with TC2 (via Direwolf):
1. Certain aspects needed for critical research are quite expensive and wasteful of other essentia, notably Tempus and clocks.
2. I use the Essentia Everything addon and it has helped a lot. Prior to Xycraft adding basic machines like Xychorium soil the green xychoridite was helpful for copper transmutation. In general be more aware and respectful of addons that might get nuked by any serious transfiguration of Thaumcraft.
3. Certain aspects are simply not being utilized sufficiently if at all (Bestia, Tenebris, Mortuus, Aer, Aqua, Lignum, Venenum). Messis would be an issue also if not for Thaumic Bees' concentrated compund. Having a good "sink" for excess essentia from common items would be helpful.
4. Taint was an excellent way for the world to go wrong. The idea of some kind of world corruption that changes things like trees, flowers, terrain, and mobs, altering the essentia of the blocks, items, and mob drops, is a good balance between the wisp spawns and TC2's tainted land.
5. I had to change some configuration with Mo Creatures to aid compatibility with Thaumcraft.
6. You were missing a critical transmutation--redstone.
7. Essentia collection and storage are too limiting later on. Using arcane glass to improve the capacity of warded jars and alembics would be a good addition later on. A "flux pipe" that connects an alembic to a jar would allow an essentia hog like a heavily enchanted helm to be stored with little to no loss. That would at least double the number of aspects you could pull from a crucible.
8. Check my post on Elemental Armor for details, but in general the goggles and traveler's boots need defense upgrades and the thaumic chestplate and leggings need special ability upgrades. The robes simply did not live up to expectations. An enchantment unique to them to increase vis efficiency would have made them worthwhile.
9. TC2's void ingots or something equivalent should come back. That's one good way to consume Tenebris. Don't worry about supply... dark xychorium and cave scorpion drops provide plenty. Mortuus from common bones, rotten flesh, etc was never an issue.
10. There are situations in Minecraft where Thaumcraft could help but does not. Village sieges could be made a lot less painful if you gave their homes a stronger door, perhaps something that ordinary zombies could not handle but angry ones could break albeit only slowly. TC Iron Golems should allow for equipment comparable to a player... perhaps an advanced version using a purified brain jar. Assigning them a marker color to patrol and guard would also help.
11. The arcane bellows needs to work with furnaces from other mods such as the coke oven, blast furnace, powered furnace, induction furnace, electric furnace, alloy furnace, etc.
12. The brain in a jar could use an upgrade also. Try surrounding an ender pearl with 4 zombie brains and 4 severed heads to make an ender brain to put in a jar.

About your musings on changes to Thaumcraft
1. The big thing on aspects has to do with supply and demand. If there are certain items or resources that players will likely make a large amount of, especially for base construction, then don't make them dependent on potentially scarce resources like zombie brains. And no, precantatio is not rare at all if you know what you're doing. I produce a lot of mine by cooking and reproducing tallow over and over again.
2. I am no stranger to magic systems, having invented three myself. The first one is DnD based and uses colors to indicate the type of effect. The second is based on an indie game called Magecraft that uses an element system not unlike Thaumcraft but with only 5 types. I expanded it eventually to 12: fire, air, water, earth, order, chaos, life, death, sun, moon, thought, heart. The last, while DnD based, uses a magical runic language where the runes are also letters of an expanded alphabet that represents nearly all basic consonant and vowel sounds.
All of these systems were used to classify spells that a mage cast using mana. Thaumcraft was not designed for that. Ars Magica already does this very well and you would be advised not to compete with it so directly. Thaumcraft revolves around alchemy, artifice, and enchantment. That theme should remain regardless of the means of pursuit.
3. You always had a system where a chunk or other specified area had an internal energy. You also had buildings like temples, obelisks, and village towers, often with nodes within. If the node graphics are that troublesome then place special blocks in buildings or the base of special trees to represent them. You might want to require a special tool for collecting such blocks.

Additional ideas:
1. I've been comparing my magic rune system to your aspect system, looking for key similarities and differences. The main reason was that I had 46 letters compared with your 47 aspects. I found quite a few direct links, some more tenuous connections, areas where several aspects were described by one rune or vice-versa, and one notable opposite meaning. The differences were expected since my runes were meant for a world quite distinct from the Minecraft world and described spells rather than objects.
Some of my runes in particular are meant to modify the meaning of other runes, inverting them or giving them a shape for example. You might want to consider modifier knowledge that you have to research from something other than analyzing items.
2. To prevent wasting aspect on research I would like to see a more alchemical research table that draws essentia from a special crucible that stores essentia for that specific purpose. That way only needed essentia is drawn. Indeterminate aspects will be attempted until they are excluded for a particular item, releasing as flux. No more losing carus, metallum, etc. en masse when you only need tempus from that clock. Also consider upgrades to either the table or crucible to improve research speed and efficiency.
3. Minecraft's experience/enchantment system leaves much to be desired. There is simply no way to gain any control over the process. TC2's Occult Enchanter helped those who used it while I use the Enchanting Plus mod to get absolute control with no additional effort. I'd like to see an intermediate system where you have to earn your way to control through research. I also want a way to convert XP to vis and vice-versa as needed and therefore I need a ton of storage. The basic capacitor just won't do anymore.
4. The repair system also needs an overhaul. The vanilla way just loses material more slowly. E+ lets me repair enchanted items for a cost that scales with the enchantment, then disenchant items to get any excess XP back. That means 1 level to repair anything regardless of damage by adding Unbreaking I, repairing, then disenchanting. It's time to bring back TC2's Thaumic Restorer, using vis to repair with bonuses from drawing key essentia from jars, alembics, etc as an option.