In an interview with Metroid Prime assistant producer Kensuke Tanabe, IGN questioned about the origin of the subtitle "Echoes".
IGN: Why is the game called Metroid Prime 2: Echoes? Does this relate to the new visor mode that lets you see sound?
Kensuke Tanabe: There is going to be an Echo Visor and you're right that it does let you see sound in certain ways, but that is not where the name came from. The name itself refers to the two planets existing simultaneously and that each one is an echo of the other.