It will probably take a while. Finding all the flags and templars is a time consuming task. If you skip the additional memories and just try to do the six main quests of each level, the tower scalling quests, and the save citizen quests, it dosent take very long at all. Give an hour per assasination...thats about 10-12 hours.
The flag quests are worthless. I entered into the game trying to complete the flag quests but once I realized that there is no reward what so ever for collecting the flags, I quickly lost interest. It was interesting for a while, and iit gets you into some hairy situations with the guards, but there is absolutley no incentive to do it. No extra ending, no concept art, no galleries. It is too much trouble just to be able to say you did it.
Since you aren't getting achievements, there's not much purpose in doing 100%.
IMO, them putting over 400 flags, like 50 templars, etc was a bit much.
I did all the missions in the cities, sinch I think fighting in the game is pretty fun, even that can be skipped. As I told my brother, just go through the game to see the story, because AC2 is amazingly better (and that isn't a slam on AC, because I loved the game).