I really didn't care for the story all that much but I really liked the designs, especialy the VF-2SS SAP with the bits, and the VF-2AJ. The Marduk mecha like the Gilgameshes were pretty interesting, kind of had a Zeon look to them. I also like the character designs (Ishtar... ::drools:: ) and Silive's tomboy personality, she's almost exactly like my best friend.
What pissed me off to no ends about it was when the Macross was destroyed at the end, WHAT KIND OF SH!T IS THAT?!