Gully, Zora Queen and Osalfa, each appear to be descendants of the Kokiri, Zoras, and Rauru respectively.
Just want to say right away that I don't see how you can assume Gully is of Kokiri descent when the game begins with you meeting his adult Hylian parents. Gully is a Hylian, same as Irene, same as Osfala, same as Impa, same as Rosso, and same as Seres. In fact, Oren is the only sage who isn't a Hylian in
A Link Between Worlds.
The issue seems to be figuring out who these Seven Sages are actually descended from in the first place.
A Link Between Worlds tells us it's the sages who sealed Ganon during the Imprisoning War and it's important to remember that we have never been shown that event once in the entire series. They did say that
Ocarina of Time depicted the events at the time of that game's release but it has since been retconned in the Hyrule Historia.
Hyrule Historia tells us that it took place on the Hero Defeated timeline after Ganon defeated Link. According to the Historia, Ganondorf took the Triforce of Courage from him and then took the Triforce of Wisdom from Princess Zelda, transforming into Ganon. The Seven Sages then sealed him away to protect Hyrule. However, several years later, Ganon returned with an army of monsters. The Imprisoning War was fought to stop him and this is when the Seven Sages from which
A Link Between World's sages are descended came along to seal the Sacred Realm.
The canon includes two separate sealings: one directly following the events of
Ocarina of Time and another that occured several years afterwards. These two sealings were performed by two
different groups of Sages; in other words, the
Ocarina of Time sages have nothing to do with the
A Link Between Worlds sages. Nothing in-game ever indicates that they do, as all reference to the ancestral sages refer to the events of the Imprisoning War when Ganon was sealed in the Dark World which did not exist at the time of
Ocarina.
From the information presented in
A Link to the Past we can see that the sages who acted during the Imprisoning War were all Hylian males, which means their descendants--the maidens--all being Hylians, too, isn't a contradiction. Neither are the sages of
A Link Between Worlds a contradiction because they are all Hylian as well, with the one exception of Oren.
How a Zora comes to be the descendant of a Hylian is unclear but
Sroa Link mentioned the only piece of information we have that could shed some light on it. Princess Ruto is clearly infatuated with Link and she seems to be serious about the marriage proposal since she even refers to herself as his fiancée seven years later. It's possible that Hylians and Zoras can produce offspring seeing as how it isn't an issue for her. And remember that she's the only child of the current king; having children would not only be something she would want, but something that is expected of her.
It could be interesting to note that the River Zoras--the grumpy looking, fireball spitting variety--only show up on the Hero Defeated timeline (with the exception of
Four Swords Adventures) while Sea Zoras--the friendly, always-getting-frozen variety--never appear in Hyrule on that timeline (they do show up in Labrynna, though). I don't have an explanation for why they would appear in
Four Swords Adventures but what of the possibility that River Zoras are the result of a Hylian and a Sea Zora mating? It's pure speculation of course but it could help explain why the River variety go on to entirely replace the Sea variety in Hyrule on an entire branch of the timeline, as well as clearing up the apparent contradiction that a Zora queen could not be descended from a Hylian sage.
Nothing in the timeline needs to be retconned at all.
A Link Between Worlds raises the question of how a Zora could be descended from a Hylain, but then what game in the series doesn't raise strange questions like that? Just because we don't have a concrete answer doesn't mean there isn't one. Everything else that is said about the sages in
A Link Between Worlds fits in to the establihsed canon with no issues and so there does not need to be a retcon, nor is
A Link Between Worlds a retcon in itself; it makes it abundantly clear that
A Link to the Past was a separate and very real event in history.