As for myself, I liked the ending. The ending is totally fitting the beginning and the general feel of the anime/manga. This anime isn't at all "feely-feely-good-abouty", but rather a serious, melodramatic and mature. The underlying themes of hope, courage, sadness, despair, sorrow, love, sex, humanity, greed, lust and malice all are well balanced and executed to a good extent.
We cannot really blame BONES for the apparent "weaknesses" [if there is any] of this particular series since they only took part in the animation, which I might add was excellent. They had no hand in the direction of what would happen in the anime.
Overall, if I am given the chance to rate this, I'd give it 8 out of 10, and 10 being excellent, etc. It is well executed, its plotline stayed on track with its underlying themes and it met my expectations at the end.
I have but one complaint and that is the many deaths in the end
It made me quite sad to have Tiz and even Third die. *_* But that is just me >_>
Bravo!