J. Michael Straczynski's (hereafter referred to as JMS) run on Amazing Spider-Man is a bit divisive; at the time it was coming out, JMS was a "superstar" writer and his take on the comic was by and large seen as a breath of fresh air. I believe the common view is that his later work on the title is not as good due largely to editorial interference and crossovers with "events" like Civil War. While it's not universally beloved, the Spider-Totem arc made it to spot #13 in CBR's "top 50 greatest Spider-Man stories." In 2009, Marvel began publishing an "Ultimate Collection" of JMS Spider-Man comics; five volumes were published, collecting everything JMS wrote for the book, rather than focus on individual storylines. As a bit of background, I purchased the Amazing Spider-Man DVD some years ago, and have slowly been working my way up through the 70's up until JMS begins his run in 2001. So unlike a reader starting fresh, I came into JMS's run having sat through a truly awful period of comics (and I'm not referring to the Clone Saga, but Howard Mackie and John Byrne's post-Clone Saga relaunch), along with pretty much everything else. Maybe it's this perspective that makes me think that JMS's first story arc is a pretty bad Spider-Man comic.
For those that don't remember or know the Spider-Totem story, here's a quick run-down. Spider-Man meets a mysterious old man with identical spider-powers, who knows his secret identity. The old man suggests that Spider-Man was always destined to get spider-powers and that the radioactive spider-bite maybe wasn't the true source of his abilities. He foils a school-shooting and becomes a High School Science Teacher at his old High School, then promptly forgets about that for awhile, as a big scary Dracula named "Morlun" appears, hunting him. Ezekial, the old-man with spider powers offers to help by giving Spider-Man a place to hide, but Spider-Man refuses. Morlun finds him, and the two fight for several issues. Finally, Spider-Man is able to trick Morlun into trying to absorb his "totem power" (or whatever it is he does), while his blood is irradiated. The radiation weakens Morlun, and Spider-Man pummels the weakened villain, and Morlun's servant shoots him. Spider-Man decides that it doesn't matter whether it was the "chicken" (the spider bite) or the "egg" (radiation?) that gave him his super powers, and goes home exhausted, where Aunt May has an extra key, and discovers that he's Spider-Man (a story for another day).
Anyway, it's a well-regarded story, and it features some truly excellent art by John Romita Jr. But as a Spider-Man story it's not very good, and it's indicative of a direction in JMS's run on the book that will continue to not work for the character. The problems with the story, in short, are that the book shifts in tone, and not for the better, that the entire "spider totem" idea is at best, a useless retcon, at worst it's actually damaging to the character, and that all established continuity is completely forgotten to allow JMS to tell the story he wants.
I'll start with the continuity issues. I'm not a super stickler for continuity as an adult reader, but JMS obviously has no interest in dealing with what's come before him at all. It's pretty well-established that Spider-Man has one of the best supporting casts in comics history, and JMS manages to use... Aunt May. It's not just that JMS doesn't feel like using Mary Jane, or Jameson, or the Stacy family, or Robbie Robertson, or Robbie's son Randy, who was rooming with Peter through most of the previous run, but who won't come back until after JMS is gone. He also doesn't want to use any Spider-Man villains, creating new, completely unimaginative characters. Morlun is clearly modeled after Dracula, but only visually and by virtue of being an immortal guy who feeds off others. There's no attempt made to connect him to Dracula, or Morbius, the vampire guy that Spider-Man has fought across various media (including cartoons) for decades. I guess it's fine that there's just a new super-powerful guy on the block that's immortal and has been around for centuries but no one has ever heard of him, it's pretty standard comic book stuff (although the least they could do is explain he's been in Soviet Russia for years or something), but it's a lot easier to just make up a new and vague force for Spider-Man to stop than it is to use what's come before in some way.
That ties into the tone problems. Along with ignoring what's come before, JMS introduces the idea of the "Spider Totem," basically that Spidey is the latest in an ancient tradition of "guys with animal powers." This mystical nonsense is not really explained, and it's basically all here to be a "everything you thought was true might not be true" style re-imagining of Spidey's origin. As alluded to earlier, at best, this garners a "so what," since it really doesn't change anything that happened, and at worst, it makes Spider-Man less special, since his being an every-man given power who helps others is kind of a big part of his deal. At one point Ezekial points out that Spidey fights a lot of animal counter-parts, while Captain America fights misguided patriots, and X-Men fight evil mutants. This is supposed to "prove" something, but really it just pulls the curtain back on how villains are/were created in comic books. The scene also confusingly has Kraven as one of the "totem" villains Spider-Man fights, which is odd, since he's not "The Lion." And don't ask me where Green Goblin, Electro, The Sandman, and the Kingpin fit into this theory. So we get this lazy, mystical "chosen one" stuff, and in addition, we get Ezekial, a rich businessman clearly designed by JRJR to be Peter Parker in his 50's. So in addition to taking away the special-ness of his origin, we get a guy with the exact same powers, to take away from the special-ness of being Spider-Man. You'd think there'd be a moratorium on guys running around with Spidey's powers after the Clone Saga, but here we are. Morlun in general is not a particularly good Spider-Man villain, because he's part of this whole mystical mumbo-jumbo, and he's just this plot point coming after Spider-Man because he eats guys with animal powers. I guess he's been slowly making his way to New York for the past decade of Spidey's superhero career (not to mention the 4 decades of real time)?
The actual story is essentially a "Morlun hunts him for a bit," followed by issues of "Spider-Man fights someone out of his league." Obviously fighting someone out of his league is nice, since it gives Peter plenty of dramatic moments to show his fighting spirit, and his never say die attitude, and again, JRJR does a nice job on the art. Of course, the whole structure is basically a slightly better drawn version of Spidey vs. Black Tarantula from 1998, three years earlier. That story is mostly forgotten now, but basically it's an improvement on this one in every way but art. BT is introduced as a threat, he begins establishing himself as a power in the New York mob, he has connections to Mary Jane's favorite new professor (she's his ex-wife), and after losing a few fights against him, Spider-Man beats him via a superhuman effort. The difference is Black Tarantula actually fits into Spider-Man's world, and he has goals beyond "kill Spider-Man." Of course, even that goal has been done, and better, in "Kraven's Last Hunt." Again, the fight scene is well done. JR's art is great, and there's plenty of good character beats from Spider-Man that are basically the real reason people like this arc. But again, this has been done, and better, in comics like Roger Stern and JR's "Nothing Can Stop the Juggernaut" story, which a great "Spidey's out of his league" fight made better by the fact that Spidey's not being chased around by a powerhouse trying to kill him: he's trying to actually protect people from a villain out of his league: he could easily say "oh well, this guy's out of my class, let the Avengers handle this one," but since Ditko's first issue, the whole deal is that Spider-Man makes an active choice to help others. This story pays lip service to that idea, as Morlun repeatedly endangers innocent plot points for Spidey to save, but it's really half-hearted, and the real focus is on Morlun chasing Spider-Man around.
Basically, "Coming Home" is a long fight-scene that tells an extremely simple story padded out for six issues at the expense of a supporting cast, interesting characters, or fun sub-plots (it does have a couple of well-staged "Spidey catches a regular crook" moments, though). That would still make it perfectly decent comic book storytelling if it also didn't feature a tone shift away from "everyman who fights street level crime" to "totemic Spider-guy who deals with magic." On the other hand, it does feature some of John Romita Jr.'s best art.
I guess the part about no sub-plots isn't quite true. Peter does begin teaching at his old High School, which is nice, but hardly the huge leap forward some fans made it out to be. He was teaching classes as a grad student after going back to school post-clone saga. He also foils a school-shooting. While it's probably a topic for another day, I'm not a fan of superheroes fighting Columbine/Virginia Tech-style school shooters. I'm fine with HYDRA attacking a school or whatever, but I find "gritty realism" like this in a Spider-Man comic to be a bit gross.