While the comic raises some points about The Federation, it does get grating after a while and seems to offer absolutely no points showing the good things that they do, making them a strawman to beat upon.
The "government bad" theme in the Coldest Equations arc.
The genocidal culture that gets nuked in the Kallifrax arc is a pretty obvious Expyof Iran. Eerily prescient if you consider ISIS.
What Might Have Been: The Federation arc was originally going to be a good deal longer, but the readers' complaints regarding some of the Author Tract tendencies led to a shortening of the story. Thus, the readers never got to see Babbage (Data) confronted about his creator's obvious shortcomings in the software and design departments, nor Lothario (Riker) getting a brief analysis of his sexual mores. (This was well after Riker had sex with a neuter...) To say nothing of the far-too-familiar-to-Trekkies argument regarding why Geordi needs a VISOR. Ironically, some readers believe they would have complained far less if the Author Tract had eventually moved on to these potentially-more-entertaining scenarios.