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Hojo wanted to breed both Aeris and Red XIII because they were two different species. He knew what breed Aeris was, but may not have known what breed Red is. It's not really revealed, but we refer to him as a lion type creature.
Hojo wanted to breed them so that the offspring would have the blood of an Ancient and longevity of Red's species so that they could experiment on the subject longer. Remember how, on the first disk, that the experiment could take like 120 years, farm beyond the specimen's lifetime or any of the scientists?