Fascinating.
I don't remember when the last time I went from "hmm... what the heck is this about?" after ep2 to "aaah, so THAT'S how it is" in ep3 so much. But there have been several big-deal revelations in this last ep, and I feel like making several predictions even up to the final climax and ending. How's that for hubris?
What this afterlife is about: Obviously, it is about people who carry over some major grudge or unresolved issue like an unfulfilled wish. As long as you haven't dealt with this, you cannot pass on.
Is "being erased" a bad thing? No. It's rather the opposite, it means that you have finally resolved your issue, and you can finally "pass on". How do we know? Because we saw it happen with Iwasawa. And she went out and disappeared in her moment of
completion and happiness. She finally found what she was looking for. She was finally able to sing the song she always wanted and even Yuri denied her in the beginning. It was no sad death, it was a _happy passing_.
How does Angel fit into this? This is the twist I liked the most. I'm pretty sure that Angel doesn't "work for god". She is just like Yuri and the others. Obviously she was Seitokaichou in her former life, and she feels that she failed. She's in this afterlife to atone, just like Yuri is in this afterlife to rebel and exact revenge. Evidence for it: Yuri's revelation that Angel is progressing just like she and her band of merrymen are.
But what about Yuri's earlier explanations? Yuri is wrong. This is the story she made up for herself, to live out her rebel+revenge issue. However, Angel's issue (keep a school safe as Seitokaichou) is diametrally opposed to Yuri (incite a revolution). Therefore they will have quickly crashed head-on, and the charismatic Yuri will have won followers where the very uncommunicative and introverted Angel could not. Which led to the situation on hand. The only one who seems to realize parts of it so far is...
What's the role of Otonashi? He will become the _mediator_ between Yuri and Angel. He was livid when they broke into Angel's apartment. He's also very curious about her and wants to know more. The upcoming triangle will be Yuri - Otonashi - Angel. All other characters are essentially irrelevant. And the role of Otonashi will be to somehow settle the issues between the two extremes of order (Angel) and rebellion (Yuri).
How will this story progress? Otonashi will learn more about both Angel and Yuri and be torn over it. I could even imagining a developing romance between them, in a true triangle fashion. He will manage to begin some form of relationship to Angel, and he'll also grow closer to Yuri while having his relationship increasingly strained with Yuri's henchmen, particularly when he continues to defend Angel.
And the ending? Otonashi will lose both Angel and Yuri by helping both of them pass on. It's his fate to reconcile both extremes with each other and helping them to leave this afterworld. However, in true key fashion, the ending will be very bittersweet: By doing so, he will also lose both girls he'll fall in love with. Unless, of course, they go for a cop-out ending of waking up out of the coma
What remains to be seen is how the "memory loss" aspect will play into this. I wouldn't even be surprised if in the end, Otonashi was the only "artificial" construct in the afterlife, created to resolve the Angel-Yuri battle. Or there's some more story on the meta-level, and the three of them somehow had dealings with each other in their former lives. Let's see.
In any case, my opinion on Angel Beats increased significantly after ep3. Let's bring it on.