Might as well say this one, even if I don't believe it to be very good.
Multiwinia, as a sequel to Darwinia, represents an almost universal shift in the aims and subject matter of games, particularly the regression (IMHO) of methods in which the player is able to interact with the game. Some essential components of the original Darwinia are exploration, discovery and creation (also key features of many early games, particularly those of the early 3D era) while the basis of Multiwinia's gameplay is pure violence for the sake of violence (as found in most mainstream commercial games of today such as the murder simulators known as first-person shooters).
The original objective of Darwinia, one of rescue and reconstruction, is replaced with meaningless killing. This analogy for the history of games is described perfectly on the
Multiwinia website: "As the years wore on however the Darwinians became ever more aggressive". Just replace "Darwinians" with "video games" and all becomes clear.
Multiwinia could be trying to convey a sense of loss of values that were important to games, but it's debatable whether it succeeds in doing this: the message is somewhat subverted by Multiwinia actually being fun.
Have I totally messed up my analysis by ignoring the ethnic cleansing of the virii in Darwinia?