Without spoiling anything, you should know before going into this series that the original two episodes that aired as "the ending" are not an ending. They have absolutely nothing to do with the ending, and quite frankly it's a little generous to say they're closely related to the show itself. Make note: you can skip the psychological trip that is the original episodes 25 and 26, and move right on to the movie that was created to replace them ( I have yet to watch it).
Secondly, as production continued, the animation studio behind Neon Genesis eventually became a little short on cash. What resulted from this was: 1) The crap final two episodes, and 2) extremely and unnecessarily long still shots wherein the characters do absolutely nothing, accompanied by random background noise. Most of the flaws I was able to find in the show itself stemmed from this dip in production value, but personally I didn't find them to be so jarring I could no longer enjoy the series.
Everyone who likes this show has their reasons, and I'm sure we can all agree that, symbolism etc. aside, Neon Genesis Evangelion is just a fun time to watch. It's a breath of fresh air when juxtaposed to the sub-par contemporary anime you've watched consecutively for months on end. The characters feel real: they rarely ever exemplify one specific character trait without stepping out of what is expected of said trait. Futhermore, they're all the most damaged fictional beings I've seen in a long while, and only seem more irreparable the closer you become with them. These fictional characters all interact in the most mesmerizing ways, and all I wanted to do was jump into their universe and join them.
The action is always fast, the art style is beautiful, and the voice acting for the English dub is fabulous. As the complex and intricate plot begins to unfold, you're often left with a thousand more questions than answers. That in itself can be frustrating for some, but it gave me incentive to watch ten episodes in a row and still want more.
Something has to be said for the maturity of this show as well, and by that I'm not referring to the violence or sexual themes. Evangelion heavily subscribes to the, "show don't tell" rule, which, to be quite honest, bumped it up to my top five after the first episode alone. It lets you think about its content without spelling it out for you, and it makes masterful use of the animated medium to place certain things in plain sight without grabbing you by the ears and forcing you to look in that direction. To give a simplified example, there is once instance where a character has sustained an injury, and the audience is expected to figure out what that is without being told it's there, if that makes sense. Another thing I have to give the director props for is knowing when to use music and when not to, along with the unique soundtrack. This is just further proof that Neon Genesis expects you to be able to figure things out for yourself, as it rarely ever plays an obviously emotional song to tell you what you should be feeling at any given moment.
What I found most riveting was the show's use of symbolism. Yes, there is the obvious aesthetic borrowing from various religious systems, but there is also a multitude of metaphors subtle enough that you wouldn't notice them unless you paused during or after the episode and gave the whole thing some consideration. Cracked glasses, for example, representing a character losing sight of what is important, or a distorted viewpoint, or maybe even something entirely different! There is endless material for discussions comparing the relationship between creator and created being, parent and child. This may be my bias as a literature major shining through, but I feel like a work of art has done its purpose if it has either provoked thought or invoked emotion in its audience.
That being said, the ending of this show did not ruin my regard for the anime in its entirety. I'm sure I'll have the same opinion once I finish the film (or is it two films?) that were created to rectify the studio's original mistakes. Chances are that if you're reading this you've already watched it, but if you haven't, I'd highly, highly recommend this one.
