It's a matter of opinions but I think they're better as characters than Shiki in various ways. Shiki is actually very similar to a lot of them, notably Alice, Morgan and Senua due to their complexity, mental state and morality. Senua and Alice are a textbook example of a character with mental illness that are just perfectly represented an done for me. Their stories are some of the most beautiful, haunting and fascinating thematically with extremely strong themses everyone should embrace. Morgan is an incredibly well-done deconstruction of a villain, one buildt on horrifying tragedy, constant mistake at recognizing a harsh truth rarely seen in fiction (some people are just rotten beyond redemption and will outright shit on you for trying to help them) which instantly makes her beyond refreshing for me. Her design is excellent, her powerset is fantastic, so is the fact that you don't get to defeat her, she dies a humiliating death that ciments her tragic status even more, she's a superb counterpart to the classic idea of Morgana Le Fay. She's a textbook example of what a tragic villain should be, right up there with the likes of Magneto or Two-Face.
Maleficent is just perfect as an antagonist, one of the best villains in cinema, both animated and live-action, yes she's much less complex than Shiki since she's a card-carrying villain but she's perfect for her role. Her design is sinister and screams evil but also beautiful and elegant, she's vicious, sadistic and cruel while talking and behaving in manners that are both dignified and condescending at the same time without feeling forced, she's a beast of pure raw power but is immensly cunning and careful in her plans, she devours the scene everytime she's on screen, she's collected but her outbursts are memorably horrifying and destructive, her dialogue drips with delicious evilness that makes what should have been cheezy delightful to hear because it's precisely her saying those lines and the final battle against her is a testament of what a good, blood-chilling and exciting climax should be. She's much more than a good villain, she's an absolute standard of what a badass, proudly evil and sadistic villain should be in terms of power, presence in the story and on-screen, aura, elegance, cunning, strength and cruelty.
Aqua and Sypha are superbly-made good characters who do everything they can to bring hope and safety to others yet have flaws that makes them reliable for everyone, more than Shiki (mainly because Shiki is a very particular character). They face horrific situations, enemies and fates that shake them but never give up, they're utterly badass and prove it more and more yet they can also be put in difficulties not simply by utterly powerful foes but by the right amount of mid-level enemies who can put them on the ropes, showing they're not invincible and need help to go further, which again makes them particulary reliable in ways even totally mundane people can relate to (which is weird cause I'm a very cynical person so I tend to get annoyed by simple lessons like "be good" but both of them manage to be engaging thanks to how they're written both as characters and in their story and it makes them considerably good for me).
Maybe that's because I knew the above before her so I already had examples of broken, insane, ruthless and complex female characters but even after seeing how complex and well-written Shiki is (and she is FAR ABOVE so-called great characters like Ellie from The Last of Us, Aloy from Horizon or Wanda from the MCU) and she definitely should get more recognition (and not simply in the Nasuverse but as a character as a whole), she doesn't reach the same level for me, she's excellent but not mind-blowing. ALL the others above have left something much stronger on me. I honestly can say they basically created a standard for me for what strong female characters should be, because they were just that good, well-made and memorable.
As for Medea, I admit, it's just me. On an "objective" degree, Shiki is better but I can't not love her more, I love her design, her voice, her powers and I'm a sucker for Greek Mythology. Same for Rin, I just think the character is an excellent, complex and more subtle tsundere. There are other characters like those two I prefer compared to Shiki (like Aoko, Princess Leia, Artoria or Ellen Ripley) but Shiki is superior to them.
