Good always triumphs over evil right? Is not that the saying? Benevolence wins out over destruction, and although both life and death are inevitable, life comes first and is on going, while death occurs only in an instance? Indeed.
As such, it makes sense, that Xerneas, Life, is seemingly at the advantage to Yveltal, Destruction, although truly speaking the two are equal. As for Zygarde, Life, like death is chaotic, and going on the law of entropy, chaos always wins out over order, although order may at times be restored. It is also of my opinion that Zygarde is weaker than the other two legendaries as of know because, similar to Kyurem, it has yet to have need to awaken its true power.
The reason Zekrom and Reshiram have a such a balanced relationship (equal stats with similar, fair spread, weakness to Dragon, resistance or Electric/Fire) is that they represent Ying and Yang, well specifically Truth and Ideals, seemingly contrary elements that are equal and interdependent. As such, their evenness is logical.
Dialga may have the advantage to Palkia and Giratina because unlike Space and Substance, which the latter two represent, Time is not malleable, that is it is unaltered, continually flowing unimpeded. In other words, while it is relatively easy to change where and what you are, it is quite hard to change when you are.
Finally, Kyogre having the advantage over Groudon would make sense. Why else would the world be covered mostly by seas, as opposed to land?
This is a rather overly in universe take on the matter, but I hope this helps
