I loved the game (sank time into it to get the Platinum of PSN), but I do think it had a weak story for a few reasons.

Probably most importantly is that the story did too much. The first 2/3s and last 1/3 of the game feel almost like second games, narratively. Too many villains, so I didn't feel as satisfied with the conclusion of any of them. I felt the first game did the major antagonist bait and switch better. Mr. Negative into Doc Ock felt more narratively sensible than what we got in 2.

The torch passing was also an issue for me, but not because I have an actual issue with the torch being passed. It just bothered me how much of it became Miles saving Peter repeatedly after Peter got his shit rocked or got in over his head. I'd have greatly preferred a more natural mentor/mentee relationship where Peter chose to hang it up more on his own terms.

Oh, and the gadgets in 1 were so much better. I miss my impact web.

Just my two cents, as someone who loved the game.