The Spider-Man suit
The Spider-Man suit is a powerful symbol of succession, goodness, and power. After Peter Parker returns and quickly thereafter retires, he hands the Spider-Man mantle to Miles Morales. Miles shares similar powers to Parker (which the suit enables both to use). In its many iterations, the Spider-Man suit is also symbol of goodness. Spider-Man fights for good and fights against bad people in the world.
Rising from the dead
A powerful motif in the book is people rising from the dead. First, Peter Parker seemingly rises from the dead to help Miles Morales contend with the Green Goblin, who incidentally also rose from the dead. Reynolds uses this motif as a way to create mystery and intrigue; he also does this to create the inciting incident in the story.
The Green Goblin suit
Unlike the Spider-Man suit, which is symbolic of succession, goodness, and power, the Green Goblin suit is symbolic of evil, death, and power. Throughout Spider-Man lore, as well as in Miles Morales, Green Goblin is an evildoer who wields a tremendous amount of power. With the help of his suit (which holds all of his power), the Goblin has killed a number of people and destroyed quite a bit. Naturally, because of this, he is one of the antagonists of the book.
Love
Another important motif in the comic book is love. In the book, readers learn that Peter Parker is in love with and has children with Mary Jane, who he leaves the life he loves to be with. Separately, Miles Morales is in love with Katie Bishop, with whom he shares his deepest secrets. Although their love is different, they bind Morales and Parker together and form the emotional heart of the story.
Don't count your chickens before they hatch
Miles Morales is an allegory for the idiom "don't count your chickens before they hatch," which means don't count on something good happening before it actually does. Specifically, Peter Parker and Miles Morales count on the Green Goblin being dead before they fully know he is dead.