Something I always enjoyed about this series is how it just kept on revealing things. There's always something new to think about or speculate over. Things kept progressing but was always some issue being put out there, and there were always more secrets hidden away just waiting to be revealed. For instance, there's the fact that Ribbons has been sitting inside a colossal, very cool spaceship all of this time along with Veda. And it isn't until the next to last episode that we finally learn what the true, complete plan that Aeolia had in mind really was.
Some time ago some fans thought that the Trans Am burst was some massive dues ex machina, but while it saved everyone's bacon I don't quite agree. For starters, it's telling that in spite of all the "understanding each other" stuff there still had to be fighting in order for necessary things to happen. You have Ali and Ribbons and his Innovades in contrast to, say, Louise and Graham and Andrei. There's also the fact that Trans Am is a limited function and even the burst only goes so far, so Setsuna can't just fly 00 around and bring healing and peace to the world without a care. The ideal is more about how humanity might grow from this point on, rather than Setsuna saving the world with GN particles. The key difference between Ribbons and Setsuna, in fact, is arguably that one considers himself a superior savior whereas the other (Setsuna), in spite of his evolution, does not.
It's also important to note that, as mentioned earlier, the affect of GN particles on consciousness was built up throughout season 2, and an observant viewer could easily conclude that 00 Raiser was stimulating brain waves and facilitating the evolution of its pilot. It wasn't surprising to me to see at least one person believing that Louise was dead, while others thought as I did that she had passed out from severe mental trauma. But the latter was clearly the case, fortunately.
The only thing I have difficulty understanding out of the whole thing is Lasse's injury, but that may be due to my own lack of research.
As for Aeolia's plan, I still like what I said at 00 forums, so I'll quote that. I should note that the idea of "aliens" in 00's future is a very debatable point, but I was dealing with it as a substantial possibility anyhow--which it is.