One thing that would nice to see in CIU would be the white and black checkered shirt chickens from CI3 that dropped coins upon killing. I think it would add some nice variety. (And it would make it more clear which chickens drop the coins)
As a newer player to CIU, I think players should be informed more thoroughly about changing the moron gun. And upgrading their ship, etc. The first few hours were challenging and difficult to understand with so much content and mechanics.
I also think that the space ship should comment lines said from older games when fighting or killing bosses to make the quote list larger in CIU.
Asteroid stages are classic, but maybe dropping some chickens on them occasionally like the feather stages may vary things a little? Or mixing various asteroids? Something to make the stages more interesting.
Perhaps food could also serve another purpose as fuel? Giving players a choice and making it used besides keys?
And lastly, maybe pausing the game when a player is typing in multiplayer? Not sure, just throwing an idea out there.