I ended Brotherhood with all its side quests (the one that came before the ending), and as usual left confused
In my opinion: He killed Lucy because she was a part of Abstergo (like the rest of the bunch) and she was going to screw desmond (pun intended of course) for the Apple of Eden. Why? Well, did you notice those cryptic emails for desmond? those emails clearly asked him to keep the new information (about a certain location they were looking for) secret from Lucy! No why would they want Lucy away from any info when she was practically helping him throughout the whole series? She was Abstergo, I believe. As they were running out of time, they had to put Desmond into a situation so that his involvement would increase and they could locate Apple of Eden as quickly as possible.
I do believe that voices in the end credits were totally new characters (the ones who were emailing Desmond perhaps) and they may be the real assassins. Well the apple of eden was clearly controlling Desmond, he killed Lucy out of intentions. And he was already seeing things (ghost like) because of extreme use of Animus. I think now his survival requires the use of Animus. Which is a good ground to make him use Animus again and if the ending was different, there would be no use of Animus any more. After all they were only looking the apple and they had fulfilled their objectives.
Now who is Eve? Remember the truth video from AC 2? The naked man and woman running out of a facility with the apple? In the end, the woman calls the man "Adam", which clearly indicates that she must be "Eve". In my opinion, they were the primary subjects of the category that Desmond belongs to (special DNA), and were the key to use the Apple (In AC Brotherhood, when Desmond moves his hand towards Apple, it recognized his "DNA"). Adman may no longer exist, and Desmond might be the only "Male" required to unlock the secrets along with a female who is a descendent of Eve, for which she will own the DNA of Eve required to unlock the secret of Apple and save the world from destruction.
With this aside, Templars are also looking for Eden to control the world (with negative methods but positive intentions, I might add) and I believe if Ubisoft wants to keep this series alive, Abstergo needs to get their hands on Apple of Eden, so that Desmond can become the assassin he is expected to become and fight an epic battle (hopefully) in a future era instead of past.
That's my theory