I don't see too much difference between the two, except for the fact that there are brighter colours used(this also makes me think he looks a little younger). I don't mind the bright colours, though. I'm sure I'll like this style.
As for TP Link looking like a girl, I don't believe that. He was totally BA. And he does look a little more mature, because it fit the style of TP, which was more realistic than some of the other Zeldas. And I'm sure SS Link will be just as BA.
I think Link didnt have very feminine features in TP. Other people say he did, but I disagree. Just because he had a 'smooth' face doesnt mean he is automatically feminine.
The Skyward sword version of Link is clearly different. The cel-shading has altered it slightly, but not much. He looks more baby faced in SS than he did in TP. It's not a bad thing though. He's still the same Link...in a matter of words.