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Just to explain this a bit for folks.
 
Front Samus: Obviously this is just "normal" samus, if you didn't get this one just go kill yourself now please
 
Back to Back Samus: This represents the part of samus that feels herself being corrupted and enjoys it they are implying an internal struggle etc...
 
Top Left Corner Samus: This is dark Samus which is essentially an evil mirror of Samus born from the remains of Metroid Prime in Prime 1 when it stole the Phazon suit.
 
Telling the difference between Dark Samus and Samus: Those of you who have played Prime 2 will probably have noticed that the visor is a good way to spot the difference between the two Samus characters. Dark Samus has a smooth Y shaped visor and "normal" samus has more of a funnel shaped visor with indents.
 
What does it mean?: In addition to putting the cap on the Prime incident in general they are telling you that all of this has had a heavy toll on Samus. Now she is not only struggling with being corrupted but with the thought that she likes it. But when you think about this even further she is struggling with this even when being faced with a very real example of what she might become (ie Dark Samus), and she still feels herself enjoying it.
 
This should paint the picture that in order for Samus to overcome the obstacles before her she not only has to address the space pirates and the impending attack on the federation but she must find a way to fight off the corruption and embrace her humanity again so she can face Dark Samus and finally close the last door in this nightmare she has been living.
 
PS - I may be reading into the cover a bit but thats what I took away from it as a player who has played both Prime 1 & 2. I think even the most hardcore fans of the rest of those games 1Up mentions would have a hard time coming up with anything as meaningful or interesting to infer from those boxarts. So I will just conclude ignorance on this one. They are completely unaware of the signifigance of the boxart (and they say as much in their blurb on it).


To Each Man, Responsibility