The final fight of Gundam 00 is symbolic for a number of reasons. It may be interpreted as a clash between the new school of Gundam (modern AUs like SEED and 00), and the old school (UC). But the nice tidbit that I noticed here is that Setsuna is actually fighting his god, the 0 Gundam that which had set his life down the path of a Gundam Meister.
Indeed, the story comes full circle from the battle-scarred boy looking up at the angelic Gundam, to the now grown-up man stabbing his former god through the cockpit. Could Ribbons have foreseen this? Kill all witnesses, his orders were, but he spared the dumbfounded boy who seemed to have witnessed a religious epiphany, because Ribbons liked the feeling of being revered. Ironically, a very human act.
In Aeolia’s original plan (i.e. the plan that would’ve been executed without Corner’s interference), Setsuna was intended to be used as a pawn, destined to be swallowed up by the beast of the world which he was to stir up. He survived, yes, but how does an abandoned pawn find the will to live? In coming up with a new goal in life, that is. Setsuna could have swallowed it up and find a more peaceful way of living, but he refused to stay down. (This is the part of him which I like the most, his sheer stubbornness, his willingness to clean up the mess he had started.) And down the long, battle-heavy road, Setsuna strikes the 0 Gundam down, and is reborn anew–in killing his old god, he affirms his power to carve his own way to the future.
Gundam 00 may have its bad points, but I choose to find a positive meaning out of it.