Yup Yukikaze is based on a very famous (in Japan at least) award-winning sci-fi novel (guess GONZO can never make as great a story as the one in Yukikaze
), so it surely has an edge over Macross Zero when it comes to plots. when GONZO's great cel-shading CG effects get combined with an award-winning story, well, I think nothing can beat it.
Besides I somehow prefer the relatively realistic air battles over transforming mechs. Yukikaze's animation just have an "authentic" feel to it instead of Macross Zero's over-the-top effects IMO.
And currently Macross Zero's story development is a bit weird IMO, with all those environmentalist sermons and strange rituals happening around XD