There are a number of reason why the story of Yiftach was selected to complement Parshas Chukas. First of all the issue of leadership. The Talmud tell us that “Yiftach in his generation was like Samuel in his generation.”
Although Yiftach was not the greatest scholar, he nevertheless was the recognized leader and a prophet. As such he was accorded the absolute support of the Halacha and the people. This support can at times appear as dogmatic as the law of the Red Heifer. However, our absolute support for our acknowledged Torah leadership is the foundation of our legal system and the transmission of Torah from generation to generation.
The second reason has to do with the battle with Sichon. Sichon was king of the Ammonites who had taken possession of lands once belonging to Moab. Sichon refused to allow the Bnai Yisroel to pass through his lands and went to war against them. Sichon was destroyed and his lands were forfeited to the Bnai Yisroel. In our Haftorah, the king of Ammon, as cousins to the Moabites, claimed legal ownership to the lands which Moshe had taken from Sichon, who had taken them from Moab.