>>4213005The Shikinami Series plot point was more to establish Asuka prior to the events of the films. All of the clones basically had to prove themselves in order to be the one chosen to pilot Unit 02 and eventually be sacrificed by Gendo with Unit 13 (it's why all the Shikinami clones are using simulations and have prototype plugsuits).
The connection between the NGE + EoE and the Rebuilds is tenuous at best, and it's ultimately easier to view the two of them as entirely different canons. There's some callbacks in the Rebuilds, but nothing that really concretely states that they're part of the same canon, just Kaworu alluding to the fact that they've been through the cycle several times at this point.
The Shikinami that is introduced in 2.0 is the same Shikinami through the end of the films, the only difference is that she gets her eyepatch after being infected with angel after the Unit 03 incident, Ritsuko even states that there's no way Nerv would be willing to lose Shikinami because she's so valuable after that infection. Clone or not, you can't replicate the angel infection by transferring it to anything, it's in our Shikinami and her alone (the OVA basically confirms that it's the same Asuka if you really need to see proof).
The Rebuilds have plenty of flaws sure, but I don't think what you listed is necessarily correct, not really sure where the Gendo jumping through parallel universes came from other than him jumping around in Minus Space so that Shinji and Mari couldn't easily get a lock on him.
tl:dr: Asuka is cute, where it's Soryuu or Shikinami, and I love her.
