What would you call this magic spot?

Well was the first thing to popped in to my head.

I would suggest Mana Well, but if you have another name for magical energy, you could use that.

 

I really like the term "Nexus"

 

*Vein (like a vein of mineral ore).
*Wellspring for positive energy, Darkdrain for bad energy uptake, or where you lose energy
*Energy Axis, if the energy is plottable on a map
*Vortex sounds chaotic, I agree with the other poster. But, that could be a 'roulette' type element. You could utilize it and get random results.

 

Hmm. I like a combination of the ideas of naming each, as with Stonehenge and the term well.

An example in our world that comes to mind actually uses the word wells which defines a place where there are springs, like "Tunbridge Wells" in the UK. In our world this refers of course to water, but in your world it could be referring to wells of magic. I also like that it feels familiar and designates it as a spot where people come or make their pilgrimage to partake.

My problem with some familiar words like vortex and genesis and the such is that, being common to readers, they'll conjure something altogether different than what I think you are reaching for here. Vortex denotes a force strong and swirling. And I imagine something large and dramatic in the case of genesis. Though, if that is how you picture these spots, then yes, that would work fine along with your descriptive prose.

A simpler word not yet mentioned could be Hub.

 

Locus, maybe? Simply meaning a place but sounding a bit fanciful. And one could do hocus-pocus at the locus.

 

I also like nexus and started to compare your situation to water- magic springs, geysers, wells. Another idea is that each location could be something different- cave, pond, mountain, forest, swamp, glacier, etc.