User blog comment:SpaceKat/assassin's creed in general/@comment-187.32.127.181-20120411044356/@comment-1153722-20120412223418
I used "Has to be" in regards to the sixth sense since I'm not 100% sure and "I suppose" only referred to the motives for having Lucy "imbedded" with Desmond's child (which are debatable), not the actual answer.
If it had been clear that Lucy was a Templar since AC2, that would have ruined the entire story. That just wouldn't have worked out and that is just looking for a reason to hate on the game.
Abstergo doesn't seem to be aware of the solar flare. They aren't "making plans for a baby," that sounds like Desmond and Lucy are settling down. They just needed Desmond's genes while not needing Desmond. Juno spoke in Brotherhood about this "Eve" as well; "Only she remains to be found." Obviously this will be shown in AC3.
Altaïr's and Ezio's Apples have been different since AC2. They have different patterns of lines on them. Look here and here for Altaïr's Apple, then here and here for Ezio's Apple. And 16 putting it in the Glyphs "because it was important" makes no sense. 16 didn't have access to enough of Ezio's memories to even see it in the Animus; he is the descendant of an illegitimate child of Ezio.
Gotta sleep now. Will get to the rest later.