Zegapain is definitely a hidden gem. If you enjoyed The Matrix then I believe this anime can offer you an experience as deep if not deeper than that trilogy, personally I'm leaning towards Zegapain.
The episodes do a great job of plunging you from slice-of-life happiness into despair, and every single episode has unpredictable plot twists that will push the symbolic knife deeper into your heart, inch by inch. Usually, I don't appreciate how nihilism is portrayed in anime and manga, but Zegapain portrayed hopelessness beautifully and dealt with it in the only proper way it could've been dealt with in the context of the world of this anime: not through fancy theories and flowery words, but through the protection of the person loved by the protagonist. Sometimes simple works best. In the oppressive world of Zegapain, where our protagonist is carrying innumerable burdens and a heavy duty, this simplicity was really a breath of fresh air. A very much needed breath of fresh air at that. Oh, and I don't mean "dumb" by saying "simple" by any means.
Unexpectedly, the character development was absolutely excellent. I'm saying "unexpectedly" because the main character is a loud rowdy type of guy. Annoying, right? Except he actually thinks about stuff pretty deeply and the changes to his character are really felt by the viewer and by the people around him. His childhood friend also has great character development at one point, but I can't say the same thing about everyone else. They kind of feel "complete", however there's a very good reason for that feeling, and it makes sense from the perspective of the plot, so the fact that everyone else doesn't get character development ends up making the story better. Amazing, huh? It's the first time I've seen something like this.
The scientific concepts were used very liberally, however the explanations were plausible enough nonetheless. At the end of the anime there were barely any plot holes left, and the ones that were left weren't serious enough to warrant criticism from me. Without spoiling anything I can say that the ending was conclusive enough on all aspects, romance included, and it left me satisfied. But I felt that it wasn't big or epic enough. We're saving the world from a mad-scientist, you know? Why not go out with a BANG?
As far as the animations go, it's above average for 2006, but it's nothing special either. I can't say that I appreciate the way the post-apocalyptic world was portrayed though. Everything is in ruins, everything is grey. I wish there were more colors, more greenery growing on the buildings, more wild animals and not just birds that pop up occasionally. Yeah, the world is supposed to feel dead, but it's just too dead. The mecha fights were meh at best too. Definitely not the strong point of this show.
That being said, if you want an interesting story that will keep you on your toes, then this is a great anime, probably approaching the levels of a masterpiece, especially if you can appreciate character development and a protagonist that grows stronger mentally and not "physically", as he's already the best pilot around from the start. But if you just want to watch robots fighting and don't plan on paying too much attention to the plot, then this isn't for you. The plot is definitely what makes this anime good, the mechas and the fights are just there for some tension.
9.4/10, best girl won (watch the post-credit scene of the last episode). MAL ratings really can't be trusted, I put off watching this for so long...