Well from the points per turn standpoint, I should have been getting a bit more per turn because of my higher earlier score, and we were at a relatively even position near the end (average of the two). You probably jumped up to the higher per turn scores earlier, so it still should be pretty close on the final score. The reason I thought that my score could be improved by a lot, is that at the end, my per turn score was up to +103 every 2 turns, and had been steadily climbing by +1 every 10 or so. This seems to point to an earlier conquest (then build) being able to score much higher. Definitely once I populated the main continent, my per turn score jumped from +20 to +40, so making that jump earlier would just mean more points overall. The offset would be a lower average to have to pull up. Haven't played enough of these types of games to really know just how much difference it makes. Will be very interesting to see.. also to see if EEK decides to play out the rest of his game in similar fashion, as it sounds like his conquest should be somewhere inbetween yours and mine.
As far as the Indians are concerned, they had to go in my game, as they had wine and gems, and wouldn't trade them to me. I think invading the mainland and leaving the Aztecs would have been the best from a scoring standpoint in my game, as the Indians had a better empire from a food standpoint. In former Indian territory I was able to build about 15 size 30 cities. None of my Aztec Isle cities was over 25 i think (too many mountains, hills and desert), and there were only 10 of them once I gave one to the English. Of course that isle was my settler factory, and did contribute mightily in that way. But leaving even the Aztects intact would have perhaps given them a shot at building a spacecraft before 2050, cutting into the final score.