In a comment to his own posting Steven writes:

One of the things I thought was particularly refreshing about Crest of the Stars was that neither side was portrayed as being "good guys". There was the crazy intelligence guy from United Mankind, but there was also Baron Febdash. Jinto and Lafiel are loyal to the Empire, as they should be, but I didn't get the impression that even they thought their side was somehow more noble, more good than the other. It's just that it was their side and they were staying loyal to it.

Unfortunately for the "refreshing" portrayal, it clashes with the reality of our world, where major conflicts had easily identifiable good and bad sides for over a century now. Moreover, such portrayal was commonly used by enemies of freedom to establish fake moral equivalence and drive the narrative. Before we know it, the concept takes root in people's minds and a government of freedom-loving people starts trying to reason with genocidal fanatics.

Also, the "refreshing" portrayal is not all that refreshing these days. For example, fighting was portrayed as senseless and driven by corrupt politicians back in Nadesico, so this angle is nothing new. Further, the "refreshing" approach is gradually taking over. I might need to gather some statistics, but it's possible that Vandread might've been the last anime where the proper concept of "enemy" was given a proper hearing, at least among the series worth watching.