there is that rumor of her being modified to be better adapted to things, since that is what the metroids do, adapt. Take this image of the fusion game´s endings, check her eye
http://www.metroid-database.com/m4/mfend2.png
About the save points Zekai, you could have checked your map, they are highlited
2nd edit.
Don´t worry guys, the games are long and troublesome if you want that 100% ending (those scans.. scanned everything..)