Fusion is set last chronologically but plotwise for Samus to be afraid was logical due to the effect of the X Parasite on her and how it weakened her like she had never been before.
Also another complaint with Other M is how Samus acted on Adam's orders where as in previous games she seemed much more independent.
Metroid Zero mission was her first mission so her being afraid was completely understandable. Other M is chronologically set after most of the titles including the Prime trilogy, in Other M she is struck down with fear when she see's Ridley, an adversary she has faced and defeated several times previously.
To take Samus from the badass of the Prime trilogy and reducing her to what she became in Other M seemed very out of place.
When you start up the game you get this!
“EARLY ACCESS! Heads up. The full might of Halo: Reach will not be unleashed until 14/09. Until then thanks for helping us iron out a few lingering wrinkles while you test drive the demands of the full experience. For now Matchmaking, Credit acquisition and Daily Challenges aren’t fully operational.”
The article does state that these are what I want no matter how unlikely, not what I think will happen. The article also contains a link to actual predictions for the show that are much more likely to occur.