Episode 25 and 26 run parallel to EoE from the start to finish. There's brief scenes in those last two episodes that show events that occur before Kom Susser Todd.Now, whether or not that makes it Better is up to you. Most people tend to prefer one vastly more then the other. There is some evidence that both EoE and the last two episodes both happen at the same time, or more specifically.....EP25/26 happen right around the time Kom Susser Todd is playing while Third Impact is going on and EP25/26 can be interpreted as everyone going through a sort of introspective hell because all of humanity is sharing souls/consciousness because of Third Impact merging everyone into a sort of mega-being/god somehow coordinated by REI/Lilith. Are you confused yet?
Asuka sitting in her Eva, Gendo coming to pick up Rei, and Misato and Ritsuko lying dead.
The latter is what really tore me up when watching Episode 25 and 26 for the first time; Just quickly showing me two characters lying dead and not bothering to even tell me what the fuck happened. And this was before EoE was even released on DVD. I still had to wait at least a year for that to happen.