I thought the conspiracies with NERV, Magi, Adam, and about Shinji's mother were interesting and I felt those episodes were the best. The problem was they went overboard on the metaphysical angst. One episode was okay I guess, but stretching it to two episodes without properly explaining what truly happened was too much, imo.
So pretty much yeah the metaphysics and the character deconstruction became the center of the show, and yeah, with the final two episodes they timeskip ahead, only alluding to real world events with a few still frames.
They did a mostly-introspection like episode like that once before, as you may recall, when Unit 01 had gone berserk meaning 400%+ synch ratio meaning the pilot's AT field breaks down and their body even liquifies... until about a month later when Shinji is finally able to reassert himself and reconstitute his body... this is in episode 20, and yeah, it's kind of important within the scifi mechanics of the show.
My question to you would be did you JUST watch the series? There is a movie, End of Evangelion... and its two halves are subtitled Episode 25' and Episode 26'.
Because infamously the series ending made a lot of people upset because we didn't get to see what happened... episode 25 happens and they tell you instrumentality has already begun... so like there is sort of an explanation in that Shinji is so mentally broken by killing his only friend, the only person who was kind to him (in any recent sense) that he just fades in and out of awareness himself and he's the main point of view character... but that's a cop out.
Realistically, I think they just ran out of budget and they were popular and hoped they'd get to make a movie / already knew they were going to get to make the movie; as much of a fanboy as I am, I don't know the definitive answer to that and I'm not sure GAINAX ever made it public anyway. I DO know that they were running into issues with censors.
But yeah, the movie "End of Evangelion" deals with finality regarding Gendo, Misato, Ritsuko, Asuka and the rest of NERV as well as what the various conspiracies were and what instrumentality is.
The first half involves some incredible action sequences, the second half does involve more metaphysics; since I actually like that stuff I wasn't complaining... but it explains what's happening and why better than the show does anyway.
I can't describe End of Evangelion as particularly satisfying because a) it's kind of a mind**** event movie and b) well, like I said it deals in finality. It is very grim, and very very dark. You also couldn't get it past Japanese or American censors... I mean they tell you they want to avoid Third Impact because it would be the end of the world. Part of that is right.
I do recommend if you watched the series in its entirety to finish it by watching the film. I make no promises that you will like it better than the episode 25-26 ending, but with that ending you only get one tiny resolution inside one character's head and it doesn't even show you what happens after, in the real world.