I don't agree with that. It heavily implied that they did get together at the ending, with Link accepting Zelda's offer and their birds flying off together. Given the fact that the Red Hylian Crest was seen on Oot Zelda's dress and the fact that Oot Zelda said that Link sounds familiar, I am certain that SS Link and Zelda are the ancestors of OoT Zelda. To say that they don't get together because of bloodline issue can be disproven in two ways:
1) Link and Zelda of Skyward Sword could have two children. One child will continue the main royal line while other child marries another knight and form a new bloodline. Over time, that new bloodline goes further and further away from the royal bloodline until it reaches Oot Link. By then, the line is dialuted enough for Link to form a relationship with Zelda
2) Not all Links are related. This is something that has proven since the time of the Wind Waker. WW Link has no blood relation to the Hero of Time, yet he has the same courage and unbreakable spirit as the Hero of Time. Ganondorf even says that he is the Hero of Time reborn. Also Demise saids that his incarnation will hunt those "who shares the blood of the goddess and spirit of the hero". Note that he didn't say blood of the hero.