I'm currently working on reorganizing the nav templates, it's still a work in progress and it'll probably take quite a bit before it's finished. The main reason for this is that we're switching to css sprites for the nav template images.
For example, the GregTech nav now already uses quite a bit of css sprites, which makes pages with the nav load faster, because all of those sprites are included in a single image, which only has to be loaded once, instead of the 200 or so images which it replaces, that had to be loaded separately.
The dilemma we're facing atm is the question, should we get rid of isometic images in the navigation templates (nowhere else). On MinecraftWiki, blocks are displayed two-dimensionally, which is what the alternative for us would be as well, instead of the isometric images.
There's pros and cons for both methods, some people prefer one or another. Isometric images are a clear indicator that you're dealing with a block instead of an item, it also gives you an idea of the shape and size of the block at first glance. A downside is that the you're cramming 3 16px images into a 16px space, which means that most of the detail is lost, which isn't true for flat 2d images.
The poll is open, so please cast your vote.