I like the old version better, because I'm used to it. Though, in aspects of design, I like the symmetry of the newer one. It seems a bit sloppily done, though.
I don't want this to turn into a religious discussion, but I think NOA was just playing it safe. I don't think they wanted to turn away people because of that design (which would be just stupid) but I guess some people are like that.
The old design actually really resembles the islamic crescent and star symbol:
http://www.success.co.il/knowledge/images/Supernatural-Islam-Moon.jpg
And Nintendo was forced to take it out upon later releases of OoT for the N64 and on the Gamecube as well. I like both designs, but I think I...