I really think the new Thaumometer scanning mechanic needs work. I am enjoying Thaumcraft 5 a lot, but there are two new dynamics that are making scanning un-fun for me.
Mainly, it used to be obvious what you'd already scanned, because you could see its aspects. You could tell when you'd checked something off the list. Not so in Thaumcraft 5 -- I have no idea what I might have neglected to scan, and no idea what research branches are locked, so I don't even have clues about what kind of things to scan to unlock the research that I don't know what it is! It's all very opaque.
The methodical approach of TC4 was frankly awful when starting a new instance. It took soooo much scanning to get a proper start. But this approach is actually less fun, because it's all failure! Mostly, when you scan something, you get nothing, even the first time. It doesn't even get ticked off a list. You'll probably scan it five more times just to make sure you scanned it once! Constant failure, no clear direction, few rewards -- I guess it's kind of like science that way...
If I could clearly tell what I'd already scanned, that would help. If I could get clues to what I still needed to scan, that would help a lot. Maybe this could play into the currently-purposeless Research Fragments? Could they reveal (but not unlock) unrevealed branches? Or suggest objects to scan? If the floating question marks disappeared when you'd scanned their item, that would even be something.
The scanning system needs more direction and/or communication, IMO, but I'm having a great time. Research puzzles are too easy, though. Maybe take some aspects away for some researches? Or penalize using the same compounds over and over? Take half the evil from scanning and add it to research notes and we're set.