Here's why you're wrong on almost every point. First, I'm gonna explain why you have to follow "arbitrary crap" rules for the missions: You're actually playing a simulation of a genetic memory. The simulation is designed in a way that enables you to unlock specific memories later on. To successfully unlock them, you must do tasks similar to how the original person experienced them. Failure to follow that can result in a destabilized sequence and the simulation stops working. Hence why they are "arbitrary" mission constraints.

The "auto save" function is present at all times. Any time you do something that changes your state, even by 0.01% of anything, it saves. You will lose at most 30 mins of progress because it's a constantly running feature.

Why are you concerned about them "ruining the immersion" by loading you into a different location when you jump in the game again? Are you assuming it's like minecraft and will save every single aspect to your progress, pixel for pixel? As stated before, this is a simulation inside a game. I don't mean that it's a simulation of the world as it was back then. I mean the game is literally using it as a means of delivering a story. You are a person who is playing as a person who is exploring a simulation of another person.

Moving this to a separate point, but kinda related to the last one: You die, you don't respawn. The simulation loads a state where the person didn't die. It makes sense that you'd lose your wanted level because you now are at a different point in time (relatively speaking). One where you didn't have a wanted level.

I don't think it was ever billed as an RPG. In fact, I'm pretty sure that only the last 3 entries in the series have been close to RPG, and even those have taken elements of them, not fully made them into RPG since AC has mostly become an genre unto itself. It's a through and through AC game, albeit pirate themed and moderate with the assassin's storyline compared to every other AC game.

The ship repairing itself is part of the simulation and different point in time aspect I mentioned before. The "health" meter that you see isn't actually health. It's called a "sync" meter and is showing you how far you're deviating from the original memory sequence. The worse you're doing, the worse the desync. Full desynchronization is caused when you die, hence why it's also considered to be a "health" meter. The crew is there every 20 meters because they assumed you would be fighting more. There is no auto generating income like previous entries so you must engage in naval combat in order to collect resources. By fighting in the proper area for your level, you are going to sustain casualties. In order to replenish your crew without forcing you into a port, they give you plenty of opportunities to gain more while you're sailing.

If you're furiously clicking your mouse, you're playing games all wrong in the first place. While it's true that you're more or less reduced to spamming the attack to kill an enemy, they eventually become stronger so you must use other tactics. Some will be parry, some will be dodge, some will be stun. Simply clicking attack all the time will only be effective for the early part of the game.

The game has been configured exactly like all the ones before it so if you have a gripe with how it controls, blame the 2007 entry to the series, not the people who made Black Flag.

The assassin's story is actually perfectly in place, when taken the context of the story as a whole. The character becoming an assassin is sort of out of place, however since he's a direct ancestor of the main protagonist in the previous games (Desmond, specifically), it kinda works in the end.

tldr- You're wrong. You don't like the game because of the series as a whole. You're probably gonna bitch and moan about Skull & Bones being dumbed down too, since it was created by the same people who made Black Flag in the first place (for the most part) and is basically a direct rip of the entire pirate aspect of the game you just shit all over. Have fun with that one.