A few weeks ago, I read this article, with a section about how reliving traumatic events can help people get over those events (for bonus points, it bring up how reliving through video games can be beneficial). This isn't a large leap to realising that Samus fighting Ridley repeatedly would mean she should be less likely to freak out after all the times she faced him in the games,* and that the utter freezing up she did during the umpteenth fight is just wrong.
Now first of all, I know this article was made well after the game, so there might be the lack of knowledge excuse, but it does confirm something a lot of use knew all along, that reliving traumatic experiences actually help get over them.** This isn't just something that triggers the memory of it (that another article brought up a while ago), that can legitimately cause a freak out. This is outright facing the trauma again. That is what Samus did when she faced Ridley before.
Anyway, this is the article I saw recently (the relevant point being the first brought up), and while this is from a humor site, it has links to proof of why it works (here, here, and here).
So even though the writers thought they were going for realism by avoiding the typical PTSD berserk mode (like in First Blood), they still got it wrong, as Samus should be almost outright over that trauma.
I'm not trying to call them hacks over this. There are plenty of other story problems to do that over. I'm just pointing out that the freakout is proven wrong.
* Counting all his forms confronted before this game, we have Metroid=1 (two if you count Zero Mission), Metroid Prime=1 (and we see him fly over twice before), Metroid Prime 3=3 (on a moph ball pipe, falling down a shaft, and destroying the third major phazon souce), and Super Metroid=1.
** Actually, this was known as far back as Ancient Greece, with an Aesop fable about a fox that got familiar with a lion, and thus got less frightended of the lion as a result. The moral "Familiarity breeds contempt" is even a noted thing in psychology.
A flashy-first game is awesome when it comes out. A great-first game is awesome forever.
Plus, just for the hell of it: Kelly Brook at the 2008 BAFTAs