Hmmm, some good suggestions so far. I'm liking the idea of having nodes be relatively rare and linked to special locations like the nodes I add to pyramids, witches huts, etc. Mechanically the aura recharges itself and I don't run into the problems I am currently experiencing, but finding a node opens up the possibility of a big boost to local aura regen.
My main issue is that nodes simply don't do a good job of recharging the aura, but having them as rare aura boosters sounds way better. And this way the lore stays intact.
* If nodes are destructable - consider allowing them to spontaneously reform: i.e. Thaumcraft should try to maintain some minimum ratio of nodes to players | loaded chunks.
* Only spawn nodes in whitelisted dimensions and dimensions that mods explicitly use an api to add themselves to: Mods like mystcraft and RFTools would probably want to use symbols to add nodes (and aura) to created dimensions, and the presence of nodes in dimensions created for technical purpose by other mods causes needless performance issues.
* While a full permissions system is out of scope and would conflict with server plugin based systems, do consider "locking" certain structures to the player that owns them. It is currently way too easy for a player with an iron capped wooden wand wandering about my base to permanently damage my nodes.