These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Tear Jerker: The Ending. Eve was already a woobie when she was created in the second game; after she finally had the chance of happiness, it was all taken away in a snap, and she even cause all the incidents to happen. It's just... Heartwrenching.
That One Boss / Wakeup Call Boss: Easily many of them are, depending on how well your DNA board is customized and how well you've kept up with upgrading your weapons.
Unfortunate Implications: Gratuitous shower scene (granted, the second game had one too), fanservicey-costumes that can get torn off enough to see her underwear, an Overdrive system usually involving Aya to take possession of a male soldier in order to defend herself...
Even more so when you realize she's actually Eve; a minor inhabiting the body of an adult, and treated by both the game and the characters as Ms. Fanservice.
The Woobie: Eve. The poor kid is in dire need of a hug. She just wanted to save her sister, but she inadvertently started a whole mess of other problems.