lifeless city (even before the symbiote infection)
There are cops, citizens, and cars in both portions of the story, civilians panic when something wrong happens
a story filled with so, so many holes,
That issue is there in SD as well
Kingpin, that's all, the rest do nice performance, even ones with bad voice
a few bad WTF? moments (Luke Cage teaching you moves you already know,
And Spider-Puppet, and he's a rookie who's over 10 years into the superhero business, etc..
ripping off Wolverine in half
With adamantium, nonsense
Only Logan, he had to make sure of some stuff
a good/bad morality system that doesn't change the endings at all
A boss fight on a helipad in range of the device, and you're forced to repeat the exact same move 12 times, do nothing else or you're dead meat
the useless appearances of Marvel superheroes
They are useful to make Spider-Man a bloody puppet even to his foe

and for funny interaction moments
You can guess why it annoys me when people say WoS was better than SD. While it has some flaws, at least you could tell that some heart and thought was put into SD (and to an extent, EoT). I never got that from WoS.
EoT is better than them both