First off, this is a really cool project, and I wish you luck on completing it.
I'm liking the nice clean look the new textures are giving TP. TP's textures were always a bit dirty, and there was in general a lot of stretching and what not.
However, there are some ways I think you can improve these textures a bit more to really make them pop/shine, while also retaining a bit more of TP's tone. I added some adjustment layers in photoshop over the images you've already posted; I basically increased the contrast, added a slight sepia filter, desaturated everything about 30% (mainly to tone down the additional color enhancements... the actual desaturation difference is probably around 15%), darkened the green on Link's tunic, increased the reds/yellows in the highlights, and increased the blues and purples in the shadows while strengthing the green midtone.
I exaggerated it a bit to show off the difference more (you'll probably want to tone it down another 10% or so), but I think it'd be worth trying a few adjustments like this over what you have so far. If not it still looks great, I'm just trying to be constructive.