I really do not think Thaumcraft should be touched too much. It would tear up balancing if we modify too many recipes. And if we do modify recipes, I recommend making an official plugin instead of using minetweaker which might be buggy. (Although the Thaumometer should be safe to tweak)
GregoriusT: Do your machines and items implement Thaumcraft aspects natively? Or is the existing aspects done entirely by Thaumcraft?
Another mod which might be a good idea is Immibis's Microblocks. I recently found out that those microblocks, unlike FMP, work with IC2 cables (Gee, I wonder where we are using those...) and can be made to work with other items, like Greg's Pipes. That would be REALLY useful to have to make builds look better.
Actually, thinking about it some more: Why don't we make an addon for Thaumcraft that adds some compatability with GregTech? I'm thinking more wands and a redo of some tech.