I like the labeling.
I am an electrician in an aluminum rolling mill, so I understand the importance of labeling the wires.
In "A Little Rage" I used a label printer that printed onto heat shrink tubing, which makes for a very neat job.
This was the first build where I used it, but on my other builds I used peel and stick numbers, which work good but the labels are a lot more professional looking.
When you have 2 joysticks, 12 player buttons, trackball, a few admin buttons, plus lighted buttons, the labeling helps out 7 fold when trouble shooting, especially when all the wires are the same color and you run them in a nice and neat bundle.
I like your idea of using clear heat shrink over regular labels, it is probably cheaper than using the special printer and special heat shrink media.