Meh... everyone else has listed all of the downsides of being in the Evangelion-verse, so I'll restrain myself here. Besides, I think it's pretty clear that the comic is meant as a light-hearted poke at the source material, not a genuine criticism.
What I will say is that the reason Evangelion seems to go over a lot of people's heads (including a lot of people in this thread) is that it isn't a mecha show. It's a deconstruction of mecha shows. Complaining about how grim and depressing it is, is like complaining about how violent and nihilistic Watchmen is, or how empty and superficial The Great Gatsby is. Neon Genesis took the tropes that made shows like Gundam popular, and turned them on their head. Why would you need children to pilot giant war robots, over professionally trained military personnel? What would be the psychological ramifications of forcing children to fight for you? Is it really that different from warlords using child soldiers in Africa? How would people deal with the impending apocalypse from an extraterrestrial, god-like threat?
In particular, I've never understood all the bashing that Shinji gets. He is a fourteen year old boy, pretty much forced into circumstances beyond his control, where he is quite literally all that stands between humanity and outright extinction. He's spent his entire life devoid of any parental love or affection, he lives and works with an entire company of dysfunctional neurotics, his own father sees him as nothing more than a pawn to be used and discarded, and he is regularly forced into situations where he is called upon to kill or take out his own friends.
I would not want to meet the person who can get through all that a well adjusted individual. That would be more than any adult could handle. To expect a fourteen year old boy to go through all that with an upbeat smile and a can-do attitude is to miss what Evangelion was about in the first place.
