(minor spoilers) Finished Act 1, and I have a big complaint
Every single story assassination in this game has taken away player agency. They are glorified cut scenes with a boss battle. You build your character for stealth and non-detection, then either get a cut scene with a single button event to progress, or end up in an epic battle with no option to approach the target your own way. This works sometimes, sure. But every damn time?
I had no actual combat abilities unlocked for the final boss of act 1. Not a single active ability (been rocking the talisman that gives extra damage for unused abilities and I avoid combat). All that for nothing.
You get everyone's story in a monolog to you before killing them in an anticlimactic button press, or a supposed-to-be-epic boss battle. Why? What happened to the sandbox approach to main story assassinations? The memory corridor for exposition if you need it. Nothing.
Also, every required exfiltration is just part of the cutscene that you have no control over. You can infiltrate all you want, then cutscene, button press, maybe a boss battle, and that's it.
Such an unsatisfying gameplay loop to build your character with one thing in mind and then basically be forced into something totally different anyway. They give you all these options for upgrades, but in the biggest moments, they don't matter.
Someone that has played the full game or at least more than me, please assure me that player agency exists in the main story assassinations of these other guys... because this shit is getting old.
“Force has no place where there is need of skill." Herodotus
Ouch. Cut scene main story assassinations are the worst. "Press 
to complete assassination." Boss battles are the second worst. I guess it's time to start buffing out Naoe for combat.
Update. One more target down. Can't do enough damage with assassination (7 health bars on boss i think), stuck in another Naoe boss battle.
In this one, I had the choice to go with Yasuke or Naoe though.
But it's still frustrating to have to cheese a mainline target because every one (so far) is a boss battle.
I suppose I could turn on Auto-Assassinate, but that feels cheaty for the first play through.
MAYBE some of this is because I'm specifically playing Canon Mode... but it feels like it's stroy driven, and not setting driven.
“Force has no place where there is need of skill." Herodotus
I chose Canon Mode also. My understanding was that it would eliminate those multiple-choice prompts of what you want to say during a cut scene. Those decision points generally make cut scenes even more unbearable although I did have a bit of fun in Origins by repeatedly choosing the flirtiest option. It didn't matter who I was talking to - man, woman, Eivor ended up fucking them all. 
In any event, Canon Mode should have no impact on whether a main story assassination is a boss battle.
The good news is that you can respec any time you want. I played Naoe katana for a while, but have been enjoying my recent Naoe Affliction Tanto build for combat that just shreds. Finally added some combat abilities. Still not my preferred way to play, especially for story relevant assassination targets.
“Force has no place where there is need of skill." Herodotus
I've been meaning to ask how assassinations are like in this game, and the original post tells me all I need to know. Assassinating main targets in most of the AC games doesn't have much replay value. Even in AC Mirage which I consider the first AC game in a while where you actually feel like an assassin the assassination missions are made to be cinematic.
I'll let you know if the other ones change. But so far, like 4 down, all "story driven theater" ... at least the latest one did let you explore the space a bit and wasn't purely cut scene or boss battle. I just don't think it's possible enough to be leveled enough with assassination skills to make it out without a boss battle.
That mission did have a 2 part infiltration from each character (and you played both) leading to the final confrontation... but replay on the assassination itself seems to be lacking.
“Force has no place where there is need of skill." Herodotus
At least (it seems like) you are free to go after dozens of side targets as you wish. And the somewhat refreshing forts also provides some replayability maybe (the daimyo don't refresh, as far as i can tell).
The game did something amazing that I've sort of been hoping for in previous games at one of the kuji kiri locations. Mid-meditation, Naoe was attacked by a very high level enemy and I had to run. Super cool for one of these cut scenes to be interrupted like that.
I still wish they would have yanked you/Desmond out of the animus mid-mission to escape a Templar base invasion in those early games.
“Force has no place where there is need of skill." Herodotus
Two more targets down. I've lost hope for replayability of the main story assassinations. Gone are the days of main target "variety packs." No idea who thought this treatment of the main story was acceptable in a franchise that used to be about approaching things your own way.
At least all the little side things are more free form, assuming you know any of the motivation for why they are targets to beginning with, considering you can't go back and read any of the letters you've found in the world.
Mirage was great for letting you approach things your own way. What happened here?
The story so far is fine, even good, for an AC game. The main target gameplay loop is absolutely spoiled by the above two complaints (lack of agency, can't re-read anything for context).
“Force has no place where there is need of skill." Herodotus