Well, ABF, I hope you're happy.

[Great Rumbler]

He doesn't actually appear until the second-to-last episode, sure,

And there's the problem. He gets mentioned in passing a couple of times, but that hardly lends him an presence. But then in the second-to-last episode who swoops in, professes his intention to get thousand of people killed to satisfy his bloodlust, and provides some mild menace until how turns into a complete puss and turns tail because of some angry, unarmed civilians. It certainly doesn't help matters that he's just a walking stereotype.

Loss -- No, Rio has to give up on her opposition to what her father wanted, I think that's significant... yes the "the Emperor isn't that bad" part is kind of lame, but still. She definitely had to give up something important.

She didn't give up anything because in the end she goes right back to where she wanted to be all along. That's hardly a sacrifice.

Noel having to face what she had done in getting that bioweapons plant running again

Throwing that in at the very end and not properly developing it would fall under lazy writing as well. It's another one of those "come out of nowhere" plot points that doesn't get its fair due because they had to cram everything into 12 episodes.

Loss of innocence for the recruits, I think.

Yes, they clearly showed their loss of innocence in the final scene where they're happy and laughing.

This, of course, makes no mention of all the little details and hints that get brushed aside. The giant skeleton? Who knows. As it stands it's just a MacGuffin. The war Felicia fought in? Who knows. Could be Rome or could be anything else. The talk about the world soon coming to an end? The only conclusion is that it was just metaphorical.

I'm sure it didn't help my disposition towards the ending much by watching it right after I finished A Certain Scientific Railgun where they pulled out pretty much exactly the same ending, which I absolutely hated.