I tried to start out with thaumcraft this time, as I thought it would be easier since I wouldn't have to dump massive amounts of items into the trash for it, but I'm coming to realize it's far more tedious now than it ever was. I've scanned every node in a 1-3 kilometer area around my base, every item I have, or have found while mining, flew around the nether and scanned everything I could find there, even ghasts and blazes (lost a few thaumometers there), and am still running out of or severely low (less than 20) on everything including primals. Sometimes the research is easy as can be and it doesn't take but a couple of rune moves and aspects to get it, other times I exhaust all my points and a few scribing tools getting close only to run out of aspects and have to leave it unfinished. What has me worried is that my save file is quickly growing in size, only for the need of research aspects, and I've barely scratched the surface. I'm worried I'm going to end up with a multigigabyte world save just to complete all the research. A massive world file that will by and large never get used.
I'm not certain what I'm doing differently than you, but I was able to get through every research from TC, TT, and MB with hundreds of each of the primals left over and a good deal of a number of many compound aspects as well. Some I did run low/out of, but it wasn't hard to synthesize more from my primals. And that's with exploring about the same area as you have said you did, and I'm certain I missed some nodes (those pesky ones underground often escape my goggled perception, especially when I'm on elevated terrain).
Honestly, the hardest part for me starting off with Thaumcraft was making my thaumometer, but that was just because I play with TiC and disable vanilla tools, so I had to get a smeltery running before I could mine the gold I needed to make it.
Hm. A few questions for you and your research strategies:
How familiar were you with previous versions of Thaumcraft? I'm finding that past knowledge of research aspects made it easy to guess what current research aspects have been for most items.
Do you count up how many runes it will take to complete a research note, and toss it if it takes too many? I usually light up the aspect it was discovered with, see how many light up, then use my past knowledge to guess how many more aspects (and thus runes) I have to play with. If it doesn't look favorable, I toss it. I've gone through up to 10 notes before finding a favorable node layout on some research notes.
How often do you re-light runes? I generally take the time to light enough runes for me to finish the research, move all the junk runes out of the way, turn off one aspect, move them into place, turn those back on, and repeat for each additional aspect I have lit up. At worst that uses 4 of the aspect used to start the research and 3 of the remainder. Once I get Research Mastery (hint: work for this ASAP!), that reduces to 3 and 2, since after moving some runes, it turns them off without you having to spend another aspect.