I never understood why one would make a giant node in TC3 unless the intent was to have thousands of crystal clusters near it. The best nodes in TC3 in my experience were small ones that were just big enough to be usable. This was because of how the whole node system in TC3 worked, larger nodes draining into smaller ones, and draining Aura from crystals in the ground that are within their range when depleted.
The problem with having a small "main" node is just that all Vis transfer causes flux. So every time you use Vis at your base you are causing flux everywhere in the outlaying areas nodes(which are highly likely not pure nodes) and after a short while you get a ton of badness in a very wide area. This is very bad specially on servers.
Yes, I know. The process used Vis from Nearby Nodes to generate a new node, too. And while those nodes combined, they lost Vis(and generated Instability), and that Vis didn't come back after they combined. The worst part of it all was that Vis was actually nonrenewable without external help, namely crystal clusters(or some bees from Thaumic Bees IIRC).
That is not true. All nodes regenerates Vis over time. But they had to be loaded to do so. Another reason why it is a bad idea to rely on a wide network of nodes for your Vis.
The best solution is indeed to make a very large pure node in the middle of your base and chunkload it. Box it inside a 3x3x3 box and put a MFR grinder on it to kill the wisps(good for farming essences too). Make lots of crystal clusters to overcharge the node which will start transforming stone in the ground into shards and store even more vis for you. Make Crystal capacitors to store even more of the overcharged Vis and essentially "enlarging" your nodes size.
Now any time you use vis in general area the vis is drawn either directly or indirectly from your big pure node. This is what you want because it is a pure node and it will get rid of flux faster, and if it does happen to spawn a wisp it will be taken care of. Also the crystal clusters and capacitors will refill it much faster to avoid causing more flux from borrowing vis from nearby nodes(Vis borrowing from a large network is VERY bad! generates a TON of flux).
My main node in my 1.5.2 Unleashed world: