Megatron's original name D-16 is a reference to the Japanese serial number of the original Generation 1 Megatron toy released by the company Takara in 1984. The letter D is short for Destron, the Japanese name of the Decepticons used in older media, while the number 16 denoted the original Megatron toy as the sixteenth release in the Japanese toy line.
Early in the film, Elita tells Orion, "You don't have the touch or the power," referencing Stan Bush's song, "The Touch", from The Transformers: The Movie (1986), which included the lyrics, "you've got the touch, you've got the power".
Elita uses the term GoBots as a pejorative. In the 1980s, Tonka's GoBots were a rival transforming toy line to Hasbro's Transformers that also included an animated series and animated film, each released within months of its Transformers counterpart. When Hasbro bought out Tonka in 1991, GoBots were then established as an alternate universe in the Transformers multiverse.
The colors of D-16 / Megatron's eyes in the film are reminiscent of an explanation that is given in one of the later Transformers comic books in the 21st century: "Yellow is the color of ignorance. I am intoxicated by lies; Orange is the color of awakening. I gradually understand destiny. Red is the color of truth. I will rise up."
At the train when D-16 and Orion were together after hiding from Dreadwing; several future Autobots can be seen. Notably Sideswipe, Wheeljack, Ironhide & Hound.