I play on PC so I can't speak much of Black Flag yet, but Origins was pretty good. Though probably not good enough to choose it over AC. All the bugs and glitches, repetitiveness, etc. I've beat it already (although it took me well over a week because the last part of the game became unplayable) and I'm bored. It's not much more than Arkham City was. Worth getting if you can but not worth sacrificing a better game for.

^ Topic. Haven't played any of the previous ones and I'm wanting to know if I'll be able to get this or if I will have to pass.

The game has a terrible score and only six topics in the forums aside from this one.
It has no hype and nearly passed completely under the radar and it's number one in the top ten games on the front page....
Somebody had to be bribed here. 

Unfortunately you've chosen the absolute worst build for bosses and multiplayer in general... Sniping is great at the beginning, stays great if you can actually get hits in between everybody else rushing in, or if you just play alone.
I'd consider respecing your skills, to be honest.

I just went through the story, did every side mission I could, farmed the warrior about a dozen times, did the pirate DLC, and started TVHM.
I'm now about half-way through that and a few missions into the newest DLC, it is by no means easy but I got a few legendaries from somebody when I played on another game so once I hit level 50 I should be set.
46 at this point, by the way.
Leveling in TVHM is extremely quick. 

Good points, and I agree with most of them.
The controls are perfectly fine in my opinion, the only problem being no way to run without climbing.
While using somebody as a shield tap the button a couple times, at least one of them will register.
There's no need for a manual crouch, we don't need a Skyrim stealth mechanic where you can dissapear in front of somebody's face.

In a game where it's been driven by story since the beginning? A lot of cutscenes is tolerable, more specifically it's expected.
All assassin's creed games have been like this, each getting a little worse.
My only complaints are how linear the game is and how unbearable some sync objectives are.

Namely two:
A naval mission where you must protect eight ships and the objective is limiting the amount destroyed to four.
Wouldn't be so hard if it didn't start you out in the very back on the line, no matter what I do I can't get ahead and when I finally do the ships are split up all over the place where I can't do a damn thing to save them.

And the one I think you're hinting at, assassinating somebody while haveing the objective to kill two other enemy militia while also preventing the death of an ally.
No matter how much I try it's not possible because he's on the right side and the others are all on the left.
I have to go out of my way to kill them which means he at least kills the optional ally, preventing the last objective which is completing both in one play.

Other annoyances include some naval missions that require hitting weak points/ gunpowder stores on larger ships.
Wasn't a problem early game but now one direct hit which would normally reveal the point destroys the ship entirely.

My frustration has made me forget the rest of the points I wanted to make. ._. 

On console you'll be prompted to download the patch as soon as you start the game up, save files would obviously be located on your hard drive.

I'm going to assume you're on PC though, right? Updates are set to automatically download when you launch the game, no notice or anything.
Chances are you already have it.
 As for your saves, they should be located in:

User > My Documents > Assassin's Creed III > SAVES
Or

C:\Users\PCName\Documents\Assassin's Creed III\SAVES

Example f the second, my PC name is just HomePC it's:
C:\Users\HomePC\Documents\Assassin's Creed III\SAVES

Did you also post this on the ubisoft forums?

Anyways, you have to target them first, as the shot is too far to automatically target them.
How to do that was answered for PS3, XBox is the same thing but with Y, and PC I'm unsure... I play on PC but I use a controller, I'd suggest going to your controls set-up in the menu or viewing the instruction manual in-game.
You'll need to find your controls for targeting and using secondary weapons. 

Yup, been happening to me too, I already dropped them a line about it, I'll tell you what they say. (If they reply at all.)
So far it seems nothing can really be done about it from our end, we just have to wait...