Swift is definitely playing with fire with this one: the Lilliputian Emperor represents the King of England at the time of the publication of Gulliver's Travels, George I. George was a strongly pro-Whig king. The King actively persecuted the Tories, hence the whole high heel/low heel thing (discussed in the Lilliputians' "Character Analysis"). The Emperor's vulnerability to manipulation by his ministers, Flimnap and Skyresh Bolgolam, implies that the actual King, George I, is too easily influenced by his favorites.
The Emperor of Lilliput also loves war, and really wants to enslave the people of his neighboring island, Blefuscu. When Gulliver refuses to help him destroy Blefuscu's freedom, the Emperor starts to hate Gulliver. This may be a reference to George I's war with France and Austria over Spanish territories in the War of the Spanish Succession.
Besides satirizing the man's government, Swift gets in a couple of quick jabs at his personal appearance: apparently George I was really unattractive (source: Robert Greenberg, Editor, Gulliver's Travels. New York: Norton, 1961, 13). This makes Gulliver's excessively admiring physical description of the Lilliputian Emperor kind of snippy.