I ask because while the current agreed-upon claimant to the Throne is D. Duarte Pio, he is the great-grandson of King Miguel I, famous for trying to steal the throne from his niece and fighting his brother, being exiled after he lost. His brother was Pedro IV of Portugal and Pedro I of Brazil and the royal family of Portugal continued with his descendants and not the ones of his brother. Had he not become Emperor of Brazil and his son, Pedro II, would've been the King of Portugal.
Basically, wouldn't if make more sense for the descendants of Pedro IV (the royal family of Brazil) to inherit the throne? I ask because I don't see that as a chance considered by basically anyone, so I'm assuming there's a reason for it to make no sense.
Pedro II himself was born in 1825, meaning post-Brazilian Independence. That means he was always a foreigner under Portuguese law, and therefore ineligible for the Portuguese throne (Article 89 of the 1826 Constitutional Chart).
As for D. Duarte Pio's legitimacy, that's a subject still hotly debated. The Migueline line was indeed disqualified following the civil war, but following the Republican Revolution, Manuel II signed the Pact of Dover, which basically reconciled the two Bragança lines and religitimized the Migueline one. The legal validity of this is still uncertain, as it's doubtful the King would have had the power to change succession laws without consulting parliament. On the other hand, D. Duarte Pio is a descendant of both the Migueline line and the Pedros line, via his mother who was a member of the Brazilian Imperial House.
Source (Portuguese): http://www.laicidade.org/wp-content/uploads/2006/10/carta-constitucional-1826.pdf