Charles Lee
-Either dump him as the villain or for gods sake, give him some more screen time to develop a personality. He goes from Haythams b**** to cartoonishly evil (and somehow becoming the final boss). Personally I'd have left out Achilles wall, or a ? on who the Grand Master was with some vague hints that it might be Adams or Washington that would have been red herrings setting up a surprise turn of Haytham on Connor when they start working together.
Iron out Connor's Near-schizophrenia and Bizarre motivations.
-He's all cheery and helpful with the random homesteaders, even on first meeting. Much laughing and back slapping to be had. Ten minutes later, the patriots want a favor and he's like "I DONT CARE, YOU TELL ME NOW WHERE THIS MAN IS" and smacking their hands away when they offer a friendly handshake in greeting.
-Similarly, he meets CL, and assumes he's responsible for the concurrent burning of his village and his mothers death. He advocates going to war, and is mouthy enough that the wise woman lets him talk to the magic eight ball, and it tells him to seek out Achilles to stop the men who did this. Okay then.
He gets his training, but then suddenly decides to ignore Achilles (and by proxy, the eight ball) and not kill the Templars. Okay, maybe he's not a blind peon. This backfires on him, teaching him you do need to kill some people to stop them. Then the latter half of the game seems to keep going on and on and on and on with him arguing about this with Achilles. He consistently keeps reverting back to a failed mentality instead of listening to the advice of people who started him on his quest WHO HAVE BEEN PROVEN RIGHT.
Cut out Faulkner and have Achilles be the grounded captain of the Aquila. Have the Aquila be the home base instead of the Homestead (Dump that map space into new missions or another town).
-Faulkner's prettymuch a tired cliche (Theres been how many PotC's now?) and gets something like six lines anyways. Achilles is more fleshed out, but could do with some more screen time. You could still have the homestead missions after a fashion by having to get the lumber to fix the ship, and some pelts to set up a front as trader . Additional missions to help Blacksmith/Doctor etc in cities would net you new weapon upgrades and such.
Start with only your tomahawk/bow/1 hidden blade. (And I consider Sequence 6 the proverbial start point of the game proper)
-And unlock the rest through missions. Rather then start with your crazy gadget loadout, earn them off the side missions (Rather then just money and clothing options). You can still earn money to buy consumables and so on, but put some gameplay rewards in.
Make lowering notoriety more difficult.
-Rather then just pressing a magic button on the wall (metaphorically), have notoriety decrease over time very gradually, or sped up by performing Trader activity (your presumed cover identity as above). Farther on in the game it should be very hard to lower though as you reach greater levels of infamy, adding to a difficulty curve.
"Area not available during mission" Get rid of it.
Assassinations should be "There's a guy here (at such and such a time even), Step to it, sonny". Put a time constraint on it if you want to discourage excessive dawdling. Leave the approach and reconnaissance open to the player. Don't handwalk them 90% of the way to it, then tell them exactly how to go about it with "Full Sync Objectives". Departures from this should be rare, not comprise 9/11 of your main storyline assassinations.
The actual straight up horrid part I would highlight is the incredibly anticlimactic and silly battle with Haytham (Press Counter to win!) after he gets the most characterization and buildup of any of the enemies (and possibly any of the characters). They set up this whole Luke vs Vader epic style clash between two proper assassins, and just throw it out in the window in what amounts to a dumb minigame. (Technically they do this with Desmond/Cross too, but at this point no one really expects anything out of the framing story)
