Audience-Alienating Premise: Rather than play as confident, badass heroine Aya Brea, the game instead has you play as an insecure amnesiac version who is constantly condescended to and lusted over by her allies despite being the only person who can save the world. Gameplay has also changed from a mix of RPG and survival horror game to a generic third-person shooter without any of the impressive mitochondria powers the player used in previous games.
Awesome Music: Even people who otherwise hate the game consider the OST, which Yoko Shimomura returned to work on, still quite good.
Best Boss Ever: The final confrontation with the Reaper, arguably the most challenging but satisfying boss in the game, even coming with a remix of the chase sequence song from the first game.
Broken Base: Aya's apparent Chickification though given that we're actually playing as Eve and not Aya, it's somewhat justified. Those who defend it do so on the basis of considering it a good and effective plot twist, those who hate it consider the twist nonsensical and poorly developed, and a poor justification for the Chickification.
Catharsis Factor: Getting to finally wail on the Reaper with the Berserker after being chased for so long is very satisfying.
Contested Sequel: Hoo boy, if you thought debates over the second game were heated, this game took it even further. While Parasite Eve II saw a divide in the fanbase how it changed up things from the first game in regards to focus on the survival horror aspects of the series while moving further from the original game's RPG mechanics, this game took it even further due to another Genre Shift to a third-person shooter, the removal of NMCs entirely from the plot, and the whole deal with Aya's Chickification. Quite a few Parasite Eve II detractors have the opinion of "At least it isn't The 3rd Birthday", and will often agree with Parasite Eve II's fans on that.
Franchise Original Sin: There has always been an element of sex appeal to Aya Brea, with her design deliberately being made to be strong AND sexy, which led to her actually being considered a sex symbol. The illustrations definitely did indeed show this aspect of her quite a lot as well and the beginning of the first game famously had her chasing after Mitochondria Eve in a rather revealing black dress. What stopped it from being distracting is that it was clear Aya was still depicted as a strong-willed and determined woman who had full control over her life and didn't take crap from anyone, while Eve is a much more insecure girl and has very little control over her situation for a good chunk of the game, while also upping the fanservice to capitalize on Aya's sex appeal, making the leering much more noticeable and distracting even before you added the squick factor of Eve being a much younger girl in an adult woman's body.
Les Yay: Gabrielle says some weird stuff about Aya wanting her, though Aya's just confused by what she's talking about, making it sound like Gabrielle's projecting.
Misblamed: Many blame Tetsuya Nomura and Motomu Toriyama for the various problems with the game's story. Toriyama because he came up with the original story concept and was scenario director and Nomura because he's Nomura. As it turns out, Toriyama only came up with a few things, like Aya's Blood-Splattered Wedding Dress and the story was heavily changed when it shifted from mobile game to a PSP title. Toriyama also did not write the new version's story, rather it was written by Toshimitsu Takeuchi. Nomura was also not available to take more of a role in the game's development, though he had suggested the idea of Clothing Damage to emphasize realism. While Hajime Tabata, the game's director, may not have come up with all of the more questionable ideas, he was in charge of and approved all the creative processes that went into the story's development.
Replacement Scrappy: Sure, killing off the popular main character your entire franchise is built around to replace them with a younger character has succeeded with the audience precisely zero times in the history of storytelling, but this time it'll work for sure! And that's to say nothing of the replacement being different enough from the original to lack the same appeal but similar enough to beg the question of why the beloved original had to die. Even if the plot twist had been handled well, it was never going to survive the remaining Parasite Eve fans watching their heroine die in the court of public opinion.
Beat the game, then think about that shower scene. Technically, Eve's still VERY much underage, and even with clone genetics being what they are, she still doesn't quite look legal...
All the Clothing Damage and suggestive moaning becomes rather disturbing when you realize it's being done with an underage girl in an adult woman's body.
Sometimes, you'll get to see the bottom of a Bean's foot; they're mouths.
Maeda's new characterization makes him sound like a genuinely disturbed sexual predator, saying things like "how sweet must your tears taste" to Aya, without a hint of sarcasm. No, they didn't turn him into a villain either. He says that affectionately.
The Reveal. 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. At least she gets a chance to live peacefully in a Twisted-less timeline at the end of the game, but that timeline was brought about thanks to a Heroic Sacrifice on Aya's part.
As if that weren't enough, remember the theme that played in the True Final Boss fight of Parasite Eve, "Someone calls me... someone waits for me..."? It comes back in the finale of Chapter 6, along with a reprise of the first game's main theme during the credits, after the aforementioned Heroic Sacrifice.
They Wasted a Perfectly Good Plot: The infamous plot twist of Aya actually being Eve is not a bad idea for a twist at all. In fact, if done in a better way, or in a different non-Parasite Eve setting altogether, it probably would have been much more fondly remembered. The problem comes down to the fact that it largely has nothing to really do with the plot of the game until the last third and any Foreshadowing for it is bogged down by a nonsensical and poorly developed story that it feels more like a last minute throw in because they realized too late that Aya's characterization was off and had to justify why at the very end.
That One 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.
Without usage of a bug, the Reaper is the biggest example of this.
Visual Effects of Awesome: Easily one of the best looking PSP titles ever made. There's really very little in the way of real time lighting, but the art direction on the textures and models gives them a detailed vibrancy not often seen on the handheld console.
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.
, along with a reprise of the first game's main theme during the credits, after the aforementioned Heroic Sacrifice.