As I understood it, E25/26 and EoE complement one another, not replace one another entirely. I think E25/26 take place as Shinji enters into Instrumentality and the sea of LCL, and the "congratulations" is representative of his ultimate decision to return to individual life in EoE.
Obviously there are a few bumps with this interpretation, but I think it works decently well. Certainly I would say E25/26 convey the ultimate message of evangelion as a whole better than EoE though - EoE completes the plot in a physical sense, but 25/26 complete it in an emotional sense, which I consider the more important of the two.
I've already watch rebuild 1 too, the new animation was nice in some bits (especially the fight against the first angel) but ultimately it was kinda skippable, I guess. Of course, in my case it's only been a week sense Eva ended, not 10 years.