I'll be honest with you, i liked the previous research mechanic better than this one. Except for the obvious exploits such as using cobble as a way of getting that first piece of research done, i thought it was overall better. I like all the aspect mechanic, but it gets REALLY frustrating when you're trying item after item after item and simply cannot get that aspect you need to make that research work. I mean, there are a LOT of aspects, and going by hit or miss can be frustrating, time consuming, and resource intensive.
One thing that COULD be done, is adding the possibility of finding research notes in thaumcraft dungeons, that automatically unlock one research that you can currently get. That way you at least have the option of, like you do with Mystcraft, of exploring the world and getting your research done that way, instead of burning random items in a research table. People who already completed all Thaumcraft research can also trade these in servers for items, as they would be quite valuable and time saving. Adding this as an option, of course, instead of making a mechanic change. Another option could be a "reverse engineer" kind of mechanic, where you take a thaumcraft item you found in a dungeon chest, and destroy it to get one research in the tree that leads towards it. I bet a lot of you have dozens of Thaumium Swords, armor, picks and axes just laying around that you found in random Thaumcraft dungeons. Well, why not reverse engineer them in order to speed up your research? This makes *sense*. If you're going from a completed research, it should be much easier to get research done than making it from scratch. How it works with most of everything.
I just might have to make that suggestion on the minecraft forums.