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.
Complete Monster: Deep Blue counts big time (at least, in the anime). While the manga depicted him as a savior of the aliens and more of a Well-Intentioned Extremist than anything, the anime established him as far more evil and malicious. Here are some of the best reasons why:
He's cold and extremely cruel, and doesn't hesitate to hurt Ichigo or any of the Mew Mews and will kill anyone who gets in his way without showing remorse. And worse yet, he doesn't show any of the feelings of either of his other alter-egos (Masaya and the Blue Knight) towards Ichigo herself despite her reluctance to fight him. Plus, he is the most depraved misogynist in any Magical Girl anime, BAR NONE.
He murders Quiche for getting in his way of attempting to kill Ichigo again, who sacrifices himself to protect her.
Moral Event Horizon: He unleashes beams from his fortress all over Tokyo that not only are powerful enough to destroy the Chimera, but also threaten to murder the other Mew Mews. Had Pie stayed loyal to Deep Blue and therefore not realized how evil he is and therefore not sacrificed himself to save them, they would've been slaughtered in a truly horrible way.
Did we mention he wants the Earth for himself and has no intention whatsoever of trying to help the aliens? That is why Quiche turns against him, at least in the show.
Oh, he crossed it before Quiche found that out. If the first thing listed isn't the crossing point, he definitely crossed it by violently swatting Masaya's memento of Ichigo away from her and then trying to kill her. This after Ichigo tried to reach out to Aoyama and see past the Deep Blue personality that had taken over and then proceeded to jump headfirst over the MEH.
In short: this is one of few instances where the monster is not the person, but the personality–Masaya and the Blue Knight are both OK guys. Not Deep Blue.
Draco in Leather Pants: Quiche. Many fans seemed to forget that his "OMG TWU WUB" for Ichigo is Stalker with a Crush played dead straight, complete with "I'll kill you if I can't have you" and "I'll kill him just because you like him better than me" moments.
Even if Deep Blue is a Complete Monster, fans have even bought him leather pants as well. It may have to do with the manga version apparently intending to help the aliens.
Foe Yay: Bu-ling/Taruto is canon and Pai/Retasu semi-canon if you squint.
Les Yay: Minto and Zakuro, to the point where it probably goes beyond Sub Text.
Macekre: They change the setting from Japan to America, despite it being probably the most Japanese show they've ever dealt with. It was initially touted by 4Kids as "Hollywood Mew Mew" (which eventually became an episode name). Al Kahn is quoted in a press release for this as having said "By the time we localize the programs, kids won't even know they're from Japan any more." They actually made episode 12 in Japan into episode 1 in America and threw it straight into Canon Discontinuity, not to mention the ending of that episode in the dub.
Mary Sue: Depending on where you draw the Mary Sue line, Berrii either comes dangerously close to this, or goes way beyond it.
Ron the Death Eater: Masaya. Sure, he may be a Stepford Smiler because he hates all of humanity, at least prior to meeting Ichigo, but he wasn't born evil, although most people who hate him seem to not be aware of- or deliberately ignore- that spoilered part, which happens after the American dub ended, and instead demonize him as a Gary Stu.