The game's dialogue hints at why you stab Lucy both Minerva and Subject 16 (once you finish the puzzles) say "she's not who you think she is" which of course confuses Desmond. Also did you notice the power cut as soon as you finished with the animus? (big hint at a spy)kurtzy23 said:Make the brotherhood more customizable. I could change their colour and thats It. Srsly I thought you would get to make them better with daggrs or one who is just really heavily armoured all I could do was give them full armour and keep upgrading their weapon. Oh god and a better ending why did I have to stab Lucy that made no sense and who the hell were those people talking in the credits. Lastley thos shop quests I have collected almost every treasure chests in the game and still haven't got all the shop quest's
Also if you're stuck on the fast poison quest you must get aconite from tackling a borgia courier
Guys talking at the end are likely William (Assassin HQ guy who Shaun and Lucy were emailing throughout the game) and someone else there.
You really need to be patient this isn't a series where the answers are just given to you by the end. They leave a lot to you to work out and keep you in suspense for the next title.