ElMariachi wrote:Her original nature is being a regular human that happened to be a clone.
No, not really.
"Let me tell you something. We, the Eva pilots, are the same as the Eva. They/we were constrained at the time of design in order not to surpass the framework/limit/box of humans."
"At the time of design", meaning, right from the start.
Asuka is like Kaworu or Rei. Kaworu is the first Angel who fell to become the Thirteenth, Rei is still an emanation of Lilith. That was their true nature all along - that they are also members of a clone series doesn't change that.
Gendo and Misato have an interesting exchange regarding that. Misato: "That's why you're treating Asuka like a disposable, Ikari Gendo?!"
Gendo: "It's because the Ayanami and Shikinami Type pilots were prepped for this purpose from the very start. Without issue."
(Please read the rest of the exchange for additional context.)
Mentioning the Shikinami and Ayanami type pilots in the same breath draws another parallel between them, and I don't think anybody doubts Rei's special nature.
Mari and Shinji are similar in that they are Metahumans, too - remember, Shinji is able to awaken Eva 01 in Ha, changing his eye color, and he is able to pilot in the first place. Mari has been around for a long time; Fuyutsuki recognizes her as "Maria of Iscariot", and she mentions that she hasn't heard that name in a long time. Notice also that there's no longer any restriction on who can pilot which Eva Unit - Asuka switches from 02 to 03 without any problem, Mari can pilot 05, 02 and 08, Shinji 01 and 13. So it's not about maternal bonds - it's the special nature of the pilots, long before any curse or Angelic "infection" kicks in, which allows them to pilot.
As for Asuka being the Ninth Angel: there's ... a lot, but it would require an extensive write-up. Trying to keep it simple: in Ha, when Asuka is "infected", pay close attention to what actually happens. Asuka sprouts wings of light, and is pulled towards the front end of the plug (the pilot chair falls away at that point). She sees something - a blue cross, with a creepy looking child's face barely visible (her "reflection"). She falls towards that blue, shining cross.
Before she reaches is, her skin is peeled off, revealing blue stuff beneath. At first glance, it would seem that she's splattered with the Ninth Angel's blue goo, but no, the blue stuff was there before. Her skin peeling away reveals what lay beneath the whole time. Later on, Ritsuko remarks that "her cellular tissue is free of any sign of contamination", but that they would never dispose of her "because she's a valuable specimen." Yet in Q, we see she has a glowing eye. That sounds like ... a really mindboggingly obvious sign of "cellular contamination" - unless, of course, that's not a "contamination", but simply her true nature shining through, which also explains why she is such a valuable specimen.
As for not being treated differently from a "regular" weapon: the Evas are divine beings too, and we see thousands of them in Shin - their divine nature doesn't preclude use as disposable weapons of war.