The Final Problem is one of the most important Holmesian stories, of course, but I can't say it's a personal favorite of mine. Part of that is just down to personal taste -- I don't enjoy angst, and the Reichenbach storyline has so much of it that it's hard to avoid and it does things to the Holmes/Watson relationship that I find unpalatable (especially in "The Empty House" when it's revealed that Holmes just let Watson grieve for three years because he didn't trust him to keep his survival a secret W H A T ?!?!) -- but some of my lack of enthusiasm just boils down to the fact that I don't find it a very well-written or interesting story in and of itself. The main thing that will make or break it for readers, I think, is whether they find Moriarty an appropriately fascinating and effective villain, and I...just don't. He comes out of nowhere, vanishes almost immediately, and we never see him do anything much. Holmes TELLS us he's incredibly clever through a bunch of general exposition, but he never does anything clever in this story that we get to see (unless you count following Holmes and Watson, which doesn't seem to me to require a supergenius). To me he's kind of a cardboard character, rushed out because Doyle needed The Best Criminal Ever to kill Holmes. But he put no work into it -- no clever plot twists, Moriarty doesn't make a single deduction, his "ruse" to get Watson to leave Holmes is as simple as it gets -- so his whole part of the story has always felt rather flat to me. Now, I recognize that this can be a feature rather than a bug for those who are interested in developing his character themselves -- he's a mostly blank slate but he's presented, as you say, as a 'dark mirror' to Holmes and there's a ton of potential there for fic writers to fill in those blanks with something far more developed and satisfying. I've never been drawn to exploring that myself but I can certainly understand the appeal. But looking just at Doyle's story, there's not much else to it besides the Holmes-Moriarty conflict. As you point out, Holmes's actions don't make much sense either, from the way he bungles the case to his cross-country journey with Watson when there were much better places to hide at home. Pretty much the only parts I enjoy are the lines of Watson's that show his loyalty and courage, and how much he loved and respected Holmes.

“Then it makes it the easier for me to propose that you should come away with me for a week to the Continent.” Why does Mary being away make it easier to whisk Watson away? Oh, when Watson says she's "away upon a visit" I assumed he didn't just mean 'she's down the street at someone else's house,' I assumed he was saying she was on a trip to visit friends/relatives, which is Doyle's standard line when he doesn't want to bother with writing her. If Mary's off on a trip to the country and Watson has been staying alone in the city to work, then if Holmes borrows Watson for a week, he expects to get him back before Mary comes home.

But the man had hereditary tendencies of the most diabolical kind. A criminal strain ran in his blood. I'm not a fan of this line. I think it's a reference to 19th century pseudo-scientific beliefs that certain people, and indeed entire ethnicities, were naturally inclined to be criminals. The idea that lineages are noble or corrupt, and that people with 'bad blood' can be 'born bad' or that particular families or races of people inherited evilness as if it were a medical condition...it's an ugly idea that was put to various racist and classist purposes, and I'm sorry to hear it coming out of Holmes's mouth here.

But, so as not to sound wholly negative, it's always a pleasure to see Holmes and Watson relying on each other in times of peril and trying to protect each other. I'm not immune to the story's emotional power on that front!