As far as the achievement resetting goes, I've done some looking in to it and apparently getting one of Thaumcraft 3's Achievements (be it "Wand of the Apprentice" or "For Your Eyes Only") causes all achievements to reset upon closing and reopening Minecraft. It gets pretty annoying to see "Press 'E' to open your inventory." almost every time I play because of some bug, especially since I also have IC2 and use its achievements (which lack this problem) as a bit of a guide on progress. Yet to do any research, so I can't say anything about that just yet.
Second, I kinda think that if the Arcane Workbench works as the straight Workbench as well then it should require a Crafting Table as well as a TC3 Table (Former on top of the latter, perhaps).
Also thirding the concept of not being able to see Aspects right away.
One more thing: Wisps don't spawn at all on Peaceful, and switching the difficulty to it causes any active Wisps to despawn like hostile mobs. Is this intentional?