Great discussion - too rare on these boards these days.
There is a lot to discuss about I Am Legend:
My wife and I both thought the movie was good for the interesting aspects it brought to screen, but for me there were multiple parts that simply did not work as shown:
1) How did the lead mutant know that if he took Fred (the mannikin), he could lead Neville into a trap?
2) If the lead mutant knew that Neville frequented the video store, why didn't he just set the trap at the video store? (my answer to this question would be that the video store wasn't as close to a shady spot as the bridge was)
3) I am so sick of stories where the lead character is knocked unconscious until (conveniently) the last 5 minutes before he'd be killed, just to manufacture a scene where the dog was killed but he wasn't. (And whoever wrote the death scene was obviously confused as to how a person would have to put down a rabid/mutant dog - you can't just overwhelm them physically and break their neck, like you could a child)
4) Characters (who should know/do better) doing STUPID stuff bother me.
* Neville not limping over to the car, thereby causing his dog to die, was ANNOYING.
He ended up limping to the car later on (and using the leg much more in the fight).
* But why did he have the leg wound in the first place? Because he was too stupid to grab the rope BEFORE he cut himself down.
He was a military man, and the movie suggested he was competent in a fight.
Why did he seem so incompetent in that scene, and the spooky dark tenement scene?
* For that matter, he had an automatic assault rifle - and he never even bagged one deer, with all the clear shots they showed onscreen? His failed marksmanship was why his dog followed the deer into that dark building, BTW.
5) He was around the mutants for 3 years, and successfully was able to outguess them and know how they think/react to stay alive while every other person (half a million?) was unsuccessful in surviving.
Yet he couldn't tell what was blatantly obvious in the scene where he bagged the female mutant? The dude was obviously pissed that he'd taken the girl. Neville wrote this down as there being no human behavior whatsoever left in the mutants. That seems like a spectacularly bad diagnosis, from the most expert in a field I can imagine (living amongst the subjects for 3+ years in mortal danger, having a huge motivation to classify their behavior properly, etc).
6) Worst glaring oversight/mistake -
what they showed at the end of the scene in Neville's car before he blacked out was the lead mutant getting pulled violently from the cab while bright lights shone. WRONG.
Since it was just the gal and he son, this turned out to be impossible.
Further, the mutants were not slowed down by an entire array of specialized UV lights - the next night it took them a couple seconds to dismantle all of them. So how did the gal have enough light to make them stop their attack on Neville the night before?
(Possible answer - they were SO organized, it was ALL in a subtle/tricky attempt to follow Neville to his home to find the female mutant.
Yeah - RIGHT.

)
7) What were the mutants eating the past couple years?
8) I agree that the introduction of the uninfected woman and her son (and by extension the walled-in human population) was jarring, questionable, and seemed like a ham-fisted way to ram their happy-ending 3rd act down a bleak hard-edged sci-fi film's throat.
9) Seriously - Neville did NOTHING to cause the female mutant to finally be cured.
The movie may as well have written a deus-ex-machina and gift-wrapped it to Neville and plopped it on the table right as they'd written the plot into a corner (retreating to the basement lab). If they'd had Neville do SOMEthing to finally get the cure - some leap of logic/deduction, etc. As I remember, the last treatment they showed Neville perform was to re-infect the female, after an unsuccessful test of the "Serum C-6a".
10) Any alternate ending that includes sentient mutants would HAVE to be prestaged by more scenes showing anything but mindless hunger/destruction.
One trap sprung by one lead mutant does not then lead to a scene where they can communicate and parlay with Neville.
Heck, if we assume that the lead mutant (and thus the captured female) were more "evolved" mutants (unsupported by the film BTW) then it begs the question - why would the female have been captured? It would have been any one of the number of less-"smart" mutants that would have been drawn to the blood bag trap.