Clay knew abstergo would be watching so he had to make things cryptic so that only Desmond could find/understand.
I took this DLC just like desmonds journey, a short back story leading up to recent events. It was first person puzzles b/c clay was stuck in the animus just like desmond. Only instead of waking up clay uploads himself into the animus core. The ending kinda reminded me of the first matrix.
I'm sorry, but this pissed me off so much. There's no way that this was Lucy's fate from the start. If it was, it wouldn't have been revealed in some mediocre DLC. I'm kind of bitter towards everything (AC Universe) now. This isn't M. Night Shamalan. everybody loved the character of Lucy and they brush her off in some lame DLC.
What I STILL fail to understand is how there wasn't more communication between Clay and Desmond in AC:R. How in the world didn't Desmond ask any of the most obvious questions, and why did Clay allow Desmond to continue to think Lucy was an assassin?
Ubisoft... You could have found another voice actress. I WOULDN'T ACTUALLY CARE if Lucy's voice was different. But to kill her because of your lack of creativity and aptitude to bring in another voice actress is just... Ridiculous.
1. The footprints were not from Lucy. They were just never removed from an early version. This has been confirmed, I'm sorry that I don't have the source. The clue in brotherhood to her Templar side was the e-mails from William (mentioned in the link below), and the timezone differences in them.
2. The Lost Archive was going to be part of the main game. (http://www.youtube.com/watch?v=4JG33LMEzKI - excellent interview, worth listening to if you haven't already.)
This would have made more sense, so try to imagine it as being on the Animus Island.
3. They couldn't elaborate greatly on Lucy in Revelations. A few people have said it seems like they haven't really had the Lucy story planned out since the start. This is possible, but I don't agree. What they haven't had planned out since the start are Brotherhood and Revelations. They needed to leave the rest of her story for AC3, so couldn't give too many details in Revelations. It's probably the same with info about Subject 16. In light of this, it's ridiculous that they would pay Kristen Bell to do one line, especially when it wouldn't cost far-off the same as a full game. I believe she also said she enjoyed working with the AC crew, and there has been no falling out or anything like that. Once more, I have to apologise, don't have the source - it's in a thread similar to this elsewhere. I'll try to find it.