I'm on the "net positive" side of things. I've been with Thaumcraft since 2. Loved 2, loved 3, wanted to love 4. Research as a mini-game?! Fantastic! Reality fell short of expectations. It was a mini-game that was fun maybe ten times, but need to be played fifty or more per new world to use the full mod. For all the new starts I've done since 4.0 dropped, I've finished the research tree only once.
The 4.1 research system is an improvement for two reasons. Firstly, the new mini-game is much more enjoyable to me. Secondly, there is now a supported option for turning off the mini-game beyond the cheat book. Both are wins.
As far as the nerfs go, they just don't seem that bad to me. The aspect scanning changes seem like a net wash to me. The arcane furnace nugget change seems like a silly unneeded nerf to a device I never used. Mana pods are whatever, every farm uses some sort of growth acceleration these days.
The tubes are slightly annoying, but the thematic change they bring is worth it IMO. You can still build an elaborate tube network, but you'll need to be around to manually turn valves and direct essentia. If you want a hands-free solution, you're stuck with those derpy little helpers I love. Designing a room to allow my brainless minions to do their job efficiently is part of the fun for me. I'd love to see them a bit brighter...
He's doing "something" with Repair, and IMO it's about damn time. When it was introduced it had a price tag. You could easily Flux up the world running multiple high repair enchants. I've been waiting for a new "downside" since 4 hit. The two ideas mentioned so far (replace with an expendable item that needs recreating, gate behind non-research content) both interest me.
In all, I've been following Azanor for years. I trust him to continue to make an awesome magic mod.