1. When Prime died, he lost color from his body just like in the 86 movie. 2. I think the Bonecrusher cameo was homeage to the whole '2 Cyclonus' debate. any one have any others?
For your #2 I think you're looking too far into it. Rather, they simply recycled character designs from the first movie (and from new characters already in combined mode...sigh).
Starscream Variations of the lines "Freedom is the right of all sentient beings" and "One shall stand, one shall fall"
The little blue trashcan at Princeton was obviously an homage to that one G1 episode where a trashcan at a factory was toppled over when Starscream was blasting the Autobots. Obviously.
i'll have to see it a second time, but i honestly didn't see THAT many. perhaps ravage's design with the missile launchers above his hind legs? i feel like there were def less g1 homages in general.
There was a Dumb & Dumber homage. The way Sam landed was just like Lloyd Christmas fell and landed on the airport tarmac.