Considering the game starts with the ending to Super Metroid, I'm not sure how much of a "prequel" you can call it.
If the subordinate/leader situation had been handled better, it could have been a much better game. But it was horrible. She felt more clingy and whiny than respectful. Oh, man, and the upgrades, that was even worse. She would literally sit there and die rather than use a weapon system that Adam hadn't given her permission to use.
Then there was the incredibly poorly handled motherhood theme throughout that game, which did nothing at all to help the characterization.
They could have done a lot, even with holding to the same basic story and the themes they wanted to use. They just needed to try subtlety, and get someone in who could actually write.