Er...I think you have it the wrong way round. Maaya's version is actually the cover. It's a self-cover because she penned the lyrics for Megumi Nakajima's version in Macross Frontier originally and then afterwards sang her own version ^^;;
I prefer Megumi Nakajima's version but I would like to hear a Megumi version with just the piano like Maaya's. I like the full strings etc. and the way it was used in the TV show was really great.