I would say that the Sly Cooper logo is an Easter egg. It's a reference to Sly Cooper and Infamous both being made by Sucker Punch.
Oh ok, I didn't realize that was the connection. An easter egg it is then!
At Alden's tower their graffit that says "Mr.D" I think that may be a reference to Dimitri from the sly series and it sort of looks like a lizard (the graffiti I mean)
At Sandover villiage there are actually 4 precursor in the stage