A "magic tower" allows expansion while fitting in with the theme. Plus, it's best if you place your node recharging pedestal and nodes on the same axis, but just at a different y-level, as your Infusion Alter. The nodes help with stability.
As for the other buildings, I try to stick with a theme that matches the use and group buildings my purpose/use. For instance, your storage should likely be central, since everything uses that, but neither Ars nor TC4 use power, so you don't need to put power next to your magic stuff. However, if you're into bees, trees, and crops, those can be somewhat magical, so they fit next to your magic stuff.
And, GT and machines need lots of power and they require/produce stuff, so items/logistics on one side of machines and power on the other.
As for materials, an idea would be to build each type of building out of a different material and/or in a different shape. Every function should have a different look/feel. For the love of god, please don't do 9x9x9 cobblestones.
Just some general ideas.