I think that best possible way to do research would be to have it be an in-world process, but this would also make it MUCH more difficult to write. What I was thinking would be to have several "mini" versions of the standard Thaumcraft crafting stations (I say "mini" in quotes because my sample of the setup is larger than all the stations except for the infusion altar) , that are specifically for research. The actual research station would no longer be a place where you would put paper and ink, but would have a slot for 2 items: standard research notes and "experiment data". The player would be able to select researches in the Thaumonomicon to get research notes like normal, and place these in the research table. In the research table, where there used to be a minigame, a list of items and aspects relating to the research would be shown (For example, if the player was researching Nitor, glowstone and torches would be shown, as well as Ignis, Lux, and Potentia). Now, the player would go to the mini-table corresponding to the type of item, and give it one combination of an item and an aspect, and the output of this table would be sent to an "analyzer table", which will take the output and generate an "experiment data sheet". Continuing with the Nitor example, the player would throw a combination like a piece of glowstone and 2 ignis worth items into the "alchemy experiment kit", a modified crucible which doesn't output items, but when these items are thrown in, it outputs some special flux gas. The gas then flows up and is collected by a "fume analyzer," which takes in the gas as well as paper and ink and generate a sheet of experiment data. The experiment is then repeated with different combinations of items and essentia, and when a number of knowledge notes from different combinations, the exact number being determined by the type of research and if the player has researched "research mastery", the player will unlock the research. (For example, the player could be required to do 4 different experiments to unlock Nitor without reseach mastery).
It would be a long, slow process, but it would be more fun than a simple minigame and would advance the idea that this is actually research.