Yes it ruined Samus, it made her look like this uncertain rookie so late in the series. She questioned everything she did, she whined about everything else and was too scared to fight Ridley? The thing she has killed 4 times already? The game was full of plot holes, uninteresting characters, made Samus look like a tool.
The people who defend this choice confuse me, it's not about looking back on old games through nostalgia fogged glasses, it's simply she was raised as a warrior, worked with the military, killed an entire race of super weapons, fought off countless space pirates, killed THEIR LEADER, she even came to kill Ridely 4 times, the guy who killed her family! And she's uncertain and cautious about her actions? She's too scared to fight Ridley again?? Well that's in cut scenes in the game she's killing things God of War style!
Even the gameplay was really altered to the point it felt like another game. I honestly don't get the weird fanboyish defense for this game, I love Metroid games all the same but that doesn't change glaring flaws. Especially in a game so hell bent on story it doesn't even do a good job of consistency. Hell even in Fusion she was focused, calculating and was very ready. She knew what had to be done and did it. Oh and the freeze pistol taking out her varia suit, that little bit just annoyed me, some low-tech pistol disables her armor while super plasma beams, lasers, heavy impacts don't? The weakest excuse I heard was "She wasn't expecting it" then Samus needs to look into better shields because that's what shields are for.
I enjoyed the game for what it was but it was not-cannon for me in any way, the story was plot-hole ridden and took a lot from fusion but fell flat on it's face