This character(?) is the physical representation of Samus' inner mind. One may also perceive it to be her conscience, but the sheer fact that Samus sees it in the form of a Waver indicates how well she listens to it. However, at one point, it gave Samus some very useful advice on fighting techniques that don't require firearms. Whether Samus will see the need to consult her inner mind again is unknown as of this point, but the sheer fact that it actually provides useful information, and may help close plotholes, is a good indication that it will one day be seen again.
It has however, been quite a while. Most other characters seem to have an inner mind as well, but they tend to show up even less than that of Samus'.