Like you said; a continuation of her current issues with the GF. I wouldn't want a reboot since most games of this generation have never been a success with reboots in terms of sales. Look at Medal of Honor, Tomb Raider, Nights; Journey into Dreams, Golden Eye, DMC. etc. With the exception of Mortal Kombat, these games might have been successful with reviews, but they failed to meet exceptations with sales.
I'm afraid that if they do make a metroid reboot, it will probably face the same fate. What they can do on one hand in terms of a reboot is give the game a graphics overhaul, with very little change in gameplay if they're going the path of either 2D, FPP, or even the open world type.