I liked your comment praising Asuka because I think she gets a lot of hate for no reason as well, but Rei is misunderstood and the best girl meme is an extreme result of people not getting her character. Rei is literally a supernatural being combined with a science experiment. Her arc is defined by her choice for humanity. Rei is not meant to be super relatable because she’s not normal in any sense of the word. Rei is an angel who's soul moves between multiple clones and has a memory and personality of the child body/clone that she is. Rei at first suffers from lack of self worth due to her absurd circumstances and she overcomes this by saving her friends and humanity against what she sees as evil as she grows to find meaning. Crushing the glasses and seemingly forcing the suicide of the mass production units are small pieces of evidence to this puzzle. Rei is choosing the good she sees in Shinji and Asuka and allowing Lilin (humanity) to continue on an unknown path rather than Gendo’s personal god complex path or SEELE’s dogmatic eugenic path for evolution. Rei rejects SEELE without them knowing of each other directly throughout the series because their path crosses once she takes control of instrumentality. Her character is about sacrifice. She was created to be used as a sacrifice for Gendo and she ultimately chooses to sacrifice herself in a way that would help her friends. 

I believe her arc and the story as a whole is meant to display the sort of positive overcome of nihilism that I think Ano probably relates to. (This last sentence is speculation because his interviews are all over the place and ultimately he doesn’t want the meaning to be explained in an on the nose way so he self contradicts himself sometimes, I simply use all the information we are given in the best way I can) Her character in some aspects is similar to Aeris/th from FF7, but an even more depressing set of circumstances and higher level of power over events. They really aren't the same for a variety of reasons, but I'm just using this comparison to help people better understand how Rei fits into the story of Evangelion.

To be fair I never got the Shinji-Rei ships or the best girl meme. It’s so obvious from any point in the series that Shinji and Asuka make better sense together. From their complimentary opposite design to their synchronization scenes. It’s obviously a complex relationship that is messy, but it also reflects their crazy circumstances and youthful understanding of the world and each other. Deep down they both want to be accepted by each other, but Asuka wants acceptance more than Shinji. Shinji is so defeatist through most of the anime it really takes until the last couple episodes and End of Eva - which compliment those same episodes - for his growth to fully realize. Shinji’s relationship with Rei is more of a friendship and doing the right thing by each other. Shinji might have been sexually attracted to her to an extent, but only in a youthful immature way. The scene showing a "naked" version of Rei, Misato, and Asuka was simply there for the angel Leliel to abuse his weaknesses at that point in the anime and doesn't reflect a Harem or something being desired by Shinji. That scene took place in episode 16 far before Shinji developed in these last episodes. 

Almost every character in Evangelion has value so to suggest she's just a piece is kind of downplaying how important that piece is to the overall story.

I liked your comment praising Asuka because I think she gets a lot of hate for no reason as well, but Rei is misunderstood and the best girl meme is an extreme result of people not getting her character. Rei is literally a supernatural being combined with a science experiment. Her arc is defined by her choice for humanity. Rei is not meant to be super relatable because she’s not normal in any sense of the word. Rei is an angel who's soul moves between multiple clones and has a memory and personality of the child body/clone that she is. Rei at first suffers from lack of self worth due to her absurd circumstances and she overcomes this by saving her friends and humanity against what she sees as evil as she grows to find meaning. Crushing the glasses and seemingly forcing the suicide of the mass production units are small pieces of evidence to this puzzle. Rei is choosing the good she sees in Shinji and Asuka and allowing Lilin (humanity) to continue on an unknown path rather than Gendo’s personal god complex path or SEELE’s dogmatic eugenic path for evolution. Rei rejects SEELE without them knowing of each other directly throughout the series because their path crosses once she takes control of instrumentality. Her character is about sacrifice. She was created to be used as a sacrifice for Gendo and she ultimately chooses to sacrifice herself in a way that would help her friends. 

I believe her arc and the story as a whole is meant to display the sort of positive overcome of nihilism that I think Ano probably relates to. (This last sentence is speculation because his interviews are all over the place and ultimately he doesn’t want the meaning to be explained in an on the nose way so he self contradicts himself sometimes, I simply use all the information we are given in the best way I can) Her character in some aspects is similar to Aeris/th from FF7, but an even more depressing set of circumstances and higher level of power over events. They really aren't the same for a variety of reasons, but I'm just using this comparison to help people better understand how Rei fits into the story of Evangelion.

To be fair I never got the Shinji-Rei ships or the best girl meme. It’s so obvious from any point in the series that Shinji and Asuka make better sense together. From their complimentary opposite design to their synchronization scenes. It’s obviously a complex relationship that is messy, but it also reflects their crazy circumstances and youthful understanding of the world and each other. Deep down they both want to be accepted by each other, but Asuka wants acceptance more than Shinji. Shinji is so defeatist through most of the anime it really takes until the last couple episodes and End of Eva - which compliment those same episodes - for his growth to fully realize. Shinji’s relationship with Rei is more of a friendship and doing the right thing by each other. Shinji might have been sexually attracted to her to an extent, but only in a youthful immature way. The scene showing a "naked" version of Rei, Misato, and Asuka was simply there for the angel Leliel to abuse his weaknesses at that point in the anime and doesn't reflect a Harem or something being desired by Shinji. That scene took place in episode 16 far before Shinji developed in these last episodes. 

Almost every character in Evangelion has value so to suggest she's just a piece is kind of downplaying how important that piece is to the overall story.