I think because if the subject matter it's good to try and keep it simple and modern looking- I think maybe if you made the pipes thinner and made it so the spheres were colored (and maybe have them glow if you want a bit of a pop?? But that may not work well with the shader) it would look neat!

I can see either all single colored or alternating color patterns looking great with this-

when it comes to art sometimes you just need to fiddle with things until it looks right.

Is it important that this be 3D? If the goal is to express the ideas as simply as possible, I suspect that requiring the user to conceptualize and navigate 3D space will introduce an unnecessary learning curve.

I had an art instructor whose favourite expression was "a solution in search of a problem". The point was that all too often someone decides what they want to do first then tries to fit it to their application. In this case, you want to do 3D graphics and shaders and are fitting it to an application that may have goals that conflict with what you want to do. Putting the whole thing in orthographic projection might be a good idea, at least.

(I'm reminded of a guy who made a video game that was supposed to be about teaching kids how to program. He basically put the ability to edit code into a first person shooter. This was not a particularly good idea because now the player had to learn FPS games AND how to code. He just figured that he knew how to play FPS games therefore everyone else does, I guess. Or maybe he didn't really think about it.)

Cayra is one of the prettier flowchart softwares I've seen if you want an example to look at.

http://i.utdstc.com/screen/windows/thumb/cayra-0-9-5-3.jpg

That looks super cool! Very appealing visuals.

Keeping what dbaumgart said in mind- if you do end up switching to 2D graphics there's a lot more you could do art and style wise! Because 2D graphics are inherently simpler you have more room to play around with patterns and shapes without it looking cluttered.

I'm not sure what your target audience is or what kind of resources you have at your disposal art-wise but if you wanted to bring more character to the game you choose a theme and base the graphics on that. Some examples:

Replace the tubes with stems/branches and instead of plain circles have a leaf grow at each point?
Replace the tubes with water pipes and have the circles become water tanks?
Replace the tubes with a dotted line and have the circles be starts?
(I don't think any of the above mentioned would work well in 3D, it would likely just look messy or confusing)
There are infinite ways you could remix the tube & sphere idea it really comes down to the feel you're going for. Just be careful not to let your graphics overpower the game itself especially since it's a learning game- the player needs to stay focused and engaged in the work, the rest should just compliment it.