Ah, yes. I will concede to you that point. EoTV!Gendo's bastardry turns out to be beneficial and his ends justified his means, which makes him actually a much more interesting character in my eyes (and something I'm hoping to maybe see a bit of in Final). From that angle Gendo is the hero of the story, the one who saw what needed to be done for the sake of humanity and did everything in his power to make it happen, even if that meant being a bastard and manipulating others. He sacrificed part of his own personal humanity in order to further the whole of the greater humanity.
At least, according to his own value system, with absolutely no regard for anyone else's choices or opinions. In that light, EoE is the true Good End because the only perceivable difference is that Shinji allowed people to have a choice, whereas Gendo would have not. There is every bit as much evidence for the idea that whoever chose not to return to the real world stayed in a blissful dream-world like many around here assume Gendo was going to give everyone in his version of Instrumentality, as there is for the idea that that's indeed what everyone got in EoTV.
In case you're wondering my logic it goes like this:
Seele's plan = open Pandora's box until the "hope" at the bottom, the end of individual consciousness, comes out/occurs.
Gendo's plan = open Pandora's box but close it (stop the process) before that point, leaving everyone mixed together as individual souls with no AT Fields separating them, a colony of very close but still individual individuals who are in a sense barely individual because it becomes difficult to tell where you end and the next person begins. Note that this end is similar enough to Seele's plan that Gendo's own description of it still reads a lot like what Seele's end is often supposed to be, the key line being that he describes it as the "merging of all souls into one" in both EoTV and EoE
. (EoTV: "All souls will become one and find eternal peace." EoE: "Merge all souls into one.") Note that what Shinji rejects in EoE is in fact Gendo's version of Instrumentality (because clearly, not everyone has truly become one true consciousness yet), and the same thing we see him accept in EoTV but without any kind of process of self-realization, just a complete sudden turn-around as if that part of himself were suddenly replaced with someone else's happiness via complementation (and who knows how he feels later after the credits have done rolling, or if we can really call him "Shinji" anymore).
EoE as it happened = as per Gendo's plan but anyone who wants to return to human existence has that option. The real
Shinji, who had a choice in the matter, chose to return, before the part of him that would have chosen to do so could be replaced (or to put it the way Gendo might have seen it, before the part of him that was defective could be complemented with a part that would have made the "right" choice), like a child becoming eternally dependent on their mother's emotional support (Gendo, EoTV: "We are only returning to our mother, who has been lost to this world.") instead of growing up and learning to find happiness on their own.
I admit to thinking all of this up just now, and I thank you two for driving me [s]up the wall[/s] to type all that up and think it all through. It's a new interpretation of the show and its endings that excites me because of its compatibility with existing parallels presented in the show, chiefly that Instrumentality, Gendo's or Seele's, EoTV's or EoE's, is the ultimate dive into your mother's basement.