You nailed it, OP. I felt the exact same about it. It's a good game, no question, but yes the side quests really bogged down my excitement of the game and felt mundane after a while, just so I can get that new power to move forward in the main story. And every time I played as MJ or Miles, I couldn't wait to get back to web swinging with Peter.
And about Batman, I always preferred Batman's combat to this. Batman felt very fluid and fresh, this feels very mechanical and repetitive. Same moveset, over and over. Enemies approach the same way in packs, so it's string this guy, fling a garbage can, pull this guy toward you, punch punch evade. Repeat.
All your positives and negatives are spot on. Great post.