As for the whole silhouette problem, the best thing is to basically add defining silhouettes to the texture like they do in Borderlands and maybe add some soft Sobel Depth Shading for the border edges. Some minor enhancements to my textures are needed, but since my textures so far have been so simple, making these little adjustments is not going to be such a problem.
So I spent most of the day writing MEL scripts for doing some UV processing on my content, also fixed up quite a few things. MEL is a very simple programming language, but it has some garbage syntax that makes it not so nice to work with. But it is simple enough and I know Maya quite well, so that is not really an issue.
I swapped out my previous highlighting solution for a simple one that I found on the Unity Asset store. Works a lot better and has some nice features built into it that I like.