You make some valid points in the list (Cavil's suicide, what about the other people having babies that might have also colonized the planet, why wasn't Daniel brought up again) but I don’t think that every thing on there is legitimate. First off, with the Head/Chip Caprica and Baltar- they weren’t seen “through the eyes of” anyone. My impression was that they were literally there (they seemed to be able to affect things physically) but only could be seen by people that they chose to allow to see them. Hence, they weren’t in anyone’s head at the end- they were just there, appearing like regular humans. Then there’s question of the “coincidence” needed to produce two “duplicate” civilizations in different galaxies. This is covered by quantum physics. The universe is gigantic, and there are infinite possibilities for differentiation. Now most people take this to mean that everything in the universe is different. But the when there are infinite possibilities for differentiation, this also means that there are an equal (and infinite) number of times where no differentiation will occur. So it is possible that the same type of planet could evolve in the same type of way with the same type of species. The odds would be low- but the universe is so big that even low odds still produce what we would consider a large number in human terms. And I felt like that was the point- that the whole journey and “god machine” was a mechanism to link the end of their own attempt with the beginning of ours. Hence “all of this has happened before, all of this will happen again.” Whether or not you buy into it, it’s still valid as far as science and science fiction goes.