If you decide to give it a try, I suggest using the advanced drafting rules. This way, all draft picks are made in the open. As far as determining tactics during the ninja phase, be sure put the spies and scouts to good use to find out who's on your side or not and play accordingly.
This game won't be fun with perfect strategic information. There are some ways to gain some information through spies/scouts and observation (weapon placement, knowing what kind of cards someone has picked, etc.), but the fun comes from guessing what the other players might be doing based on incomplete information and trying to outwit them, and then seeing if you made the right guesses and decisions.
Thanks for the response. The game look so beautiful. I'll give your advanced drafting a shot.
Is there a way to play 2P without loosing the feel of the game?