Is Daeron II’s claim to the throne purely de facto? Once Daemon is legitimate, his claim through his mother should precede Daeron’s being the elder son of their father, right? How would such a claim compare to that of the Mortimers vs. the House of Lancaster? If Daemon’s original bastard status still counts, what is the point of legitimization? Why were the Beauforts legitimized if they were excepted from the royal succession?

Let’s say for the sake of argument that, for some reason, a Great Council had been called in 184 to settle the succession. How would the various claims stack out?

• Primogeniture: clearly favors Daeron, who was born in 153 AC, whereas Daemon was born in 170 AC. (Among the other Great Bastards, Aegor was born in 172, and Bloodraven in 175). This is one of the reasons why the Blackfyres had to allege that Daeron “Falseborn” was not Aegon IV’s son – if they’re both legitimate, Daeron clearly comes first.
• Proximity: now this might favor Daemon. Both men are sons of Aegon IV, but Daeron is the son of Naerys (daughter of Viserys II), and Daemon is the son of Daena (daughter of Aegon III). Since Aegon III came first, that would indicate that Daemon’s claim might be superior. (On the other hand, just as when the Lancastrians pointed to the recency of Henry V and Henry IV as opposed to the Yorkists going back to the sons of Edward III, this could be a contested issue). However, since the Great Council of 101 declared the female line irrelevant for succession purposes, this would probably be a wash.

As to the Wars of the Roses: I would say that Daemon’s claim would be a good bit more proximate than the Mortimer claim, since Edmund Mortimer was the great-grandson of Edward III’s second son Lionel of Antwerp (through the female line) and was only heir presumptive when Richard II was deposed, and by the time you get to Henry VI vs. Richard Duke of York you’ve got a lot of interposing kings. At the same time, the Yorkists also pointed to the direct male claim through Edward III’s fourth son Edmund of Langley. 

As for the Beaufort claim, I talked about it here and here.