The colour scheme is better, I love the way Link is put next to the logo, the logo is amazing, I like the way Epona is just slightly visible, etc, it looks awesomer, you've still got your old slogan on it, the news boxes look a lot tidier and nicer, etc, etc.
So, yeah, go with the second one
.
EDIT:one thing about that second one i don't like, is the large menu headers
if you're going to stick with them i suggest using a style of text that is more suitable for them.
What are you talking about? Are you using a super-low resolution or something >_>?