Your argument is solid except for one thing:
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I think that Japan is unlikely mainly because there wasn't a large Christian conflict or presence there. 1639-1854 is pretty much impossible, since Japan was completely closed to foreigners.
That's actually not true. There wasn't any long-term Christian conflict, but there was a decently large one for a short while.
One thing most people don't know (since it is practically never mentioned outside Japanese history classes) is that the shogunate first formed using
guns. Yup. That militaristic Samurai regime that ruled the nation for hundreds of years? It wasn't founded with katanas. It was created using guns that they traded the Europeans for (and actually advanced the technology a decent amount on their own). The two most common were closely akin to the 16th century musket and something like a small hand canon.
By the end of the 16th century, it is believed that Japan had more guns than any other nation on Earth, largely due to trade.
Sometime around 1650 (after the shogunate was formed), the Tokugawa started to severely control gun production and ownership until they were eventually banned altogether. Why? Because their existence meant that it would be far easier for another force to form and oppose the new regime. They publicly justified this by claiming the sword was more civilized. But up until this point, military awards regarding gunmanship were the highest in prestige, only surpassed by taking another's head in combat.
Christian missionaries arrived in the 1540s and by the 1570s were allegedly forcing conversions using lords that had converted themselves. There were also a few uses of militaristic force on both sides during these years (the Japanese that hated the Christians and the Christians doing what they always did). And Jesuit documents from that time show that they were specifically targeting lords and other people in power as converts, to spread their influence down from there.
I can DEFINITELY see a story being worked in here, with the templars coming in and empowering a family to take control of the nation using advanced firepower. The converted lords would be newly indoctrinated templars doing what templars like to do. And then you could represent a ninja (either under the Shogun or as a third party like in the current AC games) who is opposing the secret templar takeover.
It's estimated that the missionaries converted over 300,000 Japanese before they were forced out, so there is definitely grounds for a story being established here. It would most likely have to revolve around a separate order than the assassins in AC, but they could totally do it AND include templars.
Really, I'm thinking more of a spin off than another story in this series. I highly doubt the modern-day character would be Desmond. Unless the ninja was actually middle eastern who came there following the templars or something lol. But the fact that europeans were only allowed in their specific areas in specific ports, the "blending in in plain sight" thing doesn't really work...
Now, on achievements, I think artificially increasing difficulty through achievements may not be that exciting, but it certainly can be effective. I haven't played AC2 or ACB, so I can't comment on those. But I've heard good things about the SC2 mission achievements.
I think the difference there, though, is that the star craft missions can actually become difficult (at least for people like me that suck at RTS games). Getting an achievement like that is actually something I find impressive. Sure, you can ignore them and speed through with much less difficulty. But there's something to be said in fulfilling optional objectives that are quite difficult. I think achievements in missions that require actual skill to get (and can be achieved while moving forward with your main objective) are interesting.
Some examples of different types of achievements:
Kill x droids in The Force Unleashed. Not an impressive achievement. Not hard to get. And you will probably get it simply because slicing a droid in half with your light saber is fun.
Brass Balls in Bioshock is achieved by completing the game on Hard without ever using a vita chamber (so no dying if someone hasn't played it). I find this quite impressive. Others may not, but I certainly think thats an achievement to be proud of.
Assassin's Creed--Collect all y flags, all flags, kill all templars, whatever. Not interesting. Difficult in the "Finding these things without using a guide is ridiculous" kind of way. But not impressive for any reason other than it took a lot of time. Not an interesting or worthwhile achievement.
And I would like there to be a "Fully upgraded all ultimate weapons in FFX without breaking a controller in frustration" achievement. ***** YOU BIRDS.
