Setting aside the obvious redundancy of rebooting a superhero franchise with an “origins” movie despite the fact that a perfectly fine one barely a decade old already exists, Marc Webb’s “The Amazing Spider-Man” scores over Sam Raimi’s 2002 “Spider-Man” in a number of important respects. Unfortunately it also suffers from defects that keep it from the top rank in this overcrowded genre.

Like the earlier picture, this one narrates how young Peter Parker (Andrew Garfield replacing Tobey Maguire) was bitten by a radioactive spider that left him with special powers, including the ability to climb walls, and turned him to crime-fighting after the death of his beloved Uncle Ben (Martin Sheen) at the hands of a robber. But it gives him a different romantic interest—Gwen Stacy (Emma Stone, just okay), like Mary Jane Watson from the comic pages—and a different villain to confront—Dr. Curt Connors (Rhys Ifans), a one-armed genetics researcher whose experiments cause his transformation into The Lizard. That creature is part of the comic lore, too.

While the basic elements come from the comics, though, screenwriters James Vanderbilt, Alvin Sargent and Steve Kloves have tinkered with them to give the script an emphasis on Peter’s pain over the loss not simply of his uncle, but of his father as well. They’ve added a prologue that shows Richard Parker (Campbell Scott) as a colleague of Connors who’s forced to flee some nefarious baddies with his wife Mary (Embeth Davidtz), leaving young Peter (Max Charles) with Ben and his wife May (Sally Field). It’s during their attempted escape that they were killed in a car crash. It’s his discovery of his father’s long-hidden notes that takes Peter to Connors’ lab, where he’s bitten by that spider, and also gets close to Gwen, a classmate working there as an intern.

In concocting this scenario, the scripters turn Parker’s story even more than was true in the comics into one of personal loss that’s not unlike the premise of the undervalued “Superman Returns,” which was suffused with a similar longing for home and family. And because Garfield is extraordinarily good at embodying that sense of pain at the absence of his father (as well as guilt over the death of his uncle and the responsibility he feels for Connors’ passage to the dark side), the human quality of the picture is its strongest element. (Garfield, it might be noted, is convincing as a gangly high school kid even if he’s actually in his late twenties, although it was probably unwise to cast Charles as his younger self; the tyke looks as though he should have grown up to be Maguire, not his replacement in tights.)

The choice of Gwen as Peter’s girlfriend also leads to the introduction of her father, a police captain (Denis Leary), to the mix. As a result of Lear’s typically stentorian performance, Captain Stacy becomes this version’s replacement for Jonah Jameson who, along with his paper the Bugle, is imply omitted from the plot. There’s a pro forma feeling to the material involving the Stacys, but at least playing against Stone and Leary, as well as Sheen (excellent as usual) and Field, gives Garfield some good emotive opportunities.

Ifans brings a tragic quality to Connors that works well too, in the same way that Alfred Molina brought surprising depth to Doc Ock in “Spider-Man 2.” But unfortunately the choice of villains also means that we have to put up with his alter-ego, The Lizard. In effects terms the beast is decently enough rendered. But for anyone who’s seen the fifties creature feature “20 Millions Miles to Earth,” it looks all too much like a colorized version of Ray Harryhausen’s Ymir.

That might not be so problematic were the fight scenes between it and Spidey not so disappointingly messy. In “Superman Returns” Bryan Singer opted for grandeur, going for an almost balletic quality that gave his film real beauty though (some argued) stinting on the visceral excitement. A few of the choices in the action sequences here are impressive; the use of what might be termed Spidey-vision, when the camera shows his swinging from building to building from his perspective, is a particularly nifty touch. And in general the simple motion shots of the hero winging his way across the urban landscape are fine, as is a sequence in which Spidey rescues a kid from a car dangling from a bridge. (The 3D effect, especially in the IMAX format, is nicely used here.)

But when matters shift to combat between Spider-Man and the Lizard, the visuals look more plastic and computerized. That’s especially the case in the big finale, which goes for broke with a very silly scheme by Connors to release a toxin into the atmosphere that will turn all New Yorkers into reptiles, answered by Spidey’s efforts to replace it with an antidote formulated by Gwen. The confrontation includes an especially ill-advised intervention by crane operators (coincidentally colleagues of the guy whose child Spidey saved in that car), who line up their rigs to provide the wounded hero with a direct route to the Lizard. The scene of regular Joes helping out Spidey is obviously an attempt to go Raimi’s elevated-train scene in “Spider-Man 2” one better, but while the earlier sequence was mercifully small-scaled and brief, this one is huge and labored. And unfortunately it’s characteristic of the whole overstuffed last reel.

But while its Big Moments might disappoint, the more intimate ones in “The Amazing Spider-Man” are surprisingly strong, thanks to Garfield’s deft performance. He makes the movie worth watching.

Might one suggest that some enterprising writer begin work on a biographical script about Anthony Perkins as a vehicle for Garfield? His physique is spot on, and many of his expressions are extraordinarily close to the late actor’s. It would be a perfect fit.