According to the game's director Shuyo Murata, fusing both the first and second game's story and gameplay together into one experience was the most challenging part of the game's development.
It's possible to change Ken's outfit for one of the cutscenes in-game. After obtaining the WISP subweapon and escaping the Energy Facility, taking the Ardjet down to the lava until Ken starts complaining, and repeating 3/4 times, will have Ken remove the top part of her jumpsuit.