Great post OP! I hadn't really thought much about the stealth gameplay possibilities.
I agree with others that AC might not be the ideal to aim for in terms of stealth. For me, if the stealth in this game is comparable to Saboteur (last gen) or MGSV (this gen), this game could be amazing. When you think about it, MGSV might be the better comparison for this game. In MGSV, you could play the game going in loud with weapons that had a great deal of firepower. Or, you could go the stealth route and do every mission and side quest using tranquilizers, sniping from Quiet and (later on in the game) the interesting (albeit absurd) Fulton recovery system.
In my opinion, the stark contrast between playing loud in MGSV and using stealth really made the game unique. Using the game mechanics and the upgrade system for various stealth items (like tranquilzer sniper rifles and the Fulton system), you could go into heavily-guarded fortresses and use stealth to take out the entire place. Honestly, by the end of the game, fully-upgraded stealth was really overpowered. I would go into a base with 50 soldiers, and 15 minutes later, all 50 of them (plus every piece of equipment I could salvage) would be fultoned to my base.
If this game has a great contrast between the samurai style and the ninja styles, this could be a very immersive and memorable game.