Honestly, I've seen Eva twice now, I own the Platinum series Directors cut DVD set, and I've seen End of Eva once, and I can say this with full certainty that the show is extremely confusing and feels like it's really confusing for the sake of being confusing.
I mean, it's been stated a lot that Anno was apparently deeply troubled when he created the series. As well, the original plan was for the final battle to be a much more straight forward thing with much less in the way of phycho-analysis and abstract themes. The finale had nothing to do with Instrumentality originally and was going to be a straight-up action fest Robot Battle but around episode 14 they started to run out of money and by episode 18 the money well was bone dry. That's why the Psychology stuff was amped up in the end and why episodes 25 and 26 were all apparently in Shinji's head. I just looked some of this up to verify I'm on the right track with this and I found articles backing it up.
So, it honestly wasn't the perfectly executed masterpiece of a man with a cohesive vision, it was more of a depressed person's outlet for his frustrations. That can be an artform all to itself, I'm not denying that a troubled person can channel that into an artistic vision, but whatever vision he had was hobbled by a dwindling budget. I know EoE had a budget and was more of a proper conclusion to the series, but by that time they'd already written all of the overtly psychological stuff from episodes 18+ that had to be taken as canon going into the film, so there was always going to be some confusion.
One thing the original rough series outline says is that there was originally going to be a final battle where the last Angel was killed and the conspirators in SEELE/NERV were destroyed and all their machinations were too. All the secrets were going to be revealed to the veiwer too, no ambiguity.
Human Instrumentality as presented in the final version of the series was also not here from what I can see. SEELE and Gendo's plans are not elaborated on in the rough outline but are referred to as "Human Completion" which sounds more like Evolution/Perfection of humanity than the community goo that we ended up getting. This possibility is supported by the fact that every chance Anno himself has gotten to try to redo the story has had "Instrumentality" be an evolved state rather than puddle of Goo.
The PS2 games for example, which Anno directly helped in writing, tried to reconcile the two ideas (Puddle of goo + Evolved Being) and basically try to act like this was how it was in the TV series too, you were just never told it. It states that Gendo and SEELE's ACTUAL plan for instrumentality was that they would be the only ones to become Puddles of Goo, everyone else would just die, and then the goo would merge with Eva Unit 01 thus creating a God Like Being with an immortal Eva/Angel body and a collective human soul. They'd then destroy the Spear of Longinus and be perfect. Gendo intended to betray SEELE however and it would be just he and Shinji who melt into goo and merge with Unit 01. Since Yui's soul is already in Unit 01, this would effectively reuinte the 3 of them.
Now however, according to the Eva Wiki, the Rebuilds took the opportunity to fully redo the concept closer to straight up Evolution/Perfection as all signs currently point to that being the plan in the 3 movies released thus far.
So… yeah, sorry. I think the series is honestly a mess after episode 18, and despite some amazing animation (Asuka Vs. the Mass Production Evas = <3) this includes End of Evangelion.
Reading up on the production of the series as I just did tho, I'm more interested in the Rebuilds now as it does appear they may be making the Rebuilds closer to the original plan, which might explain why I keep hearing that the 3rd movie is such a radical departure from the TV series. In fact, according to the Wiki, the 2nd movie ends roughly where episode 19 would have been in the TV series before going into all-original territory in the 3rd movie. The budget was officially dry as of episode 18. I highly doubt that is a coincidence.