As one of the long time play testers of Breeding Season and someone that spent way too much time on finding optimal strategies for "beating the game" that invariably ended up being some kind of derp farming; I can say that you can absolutely avoid derp farming being the optimal strategy or even a viable suboptimal strategy in general.
Basic problem of the structure of inheritance that Breeding Season and Breeders or Nephelym and Portals of Phereon have is that they don't properly implement recessive inheritance patterns. In the real world, the major problem with severe inbreeding is that it concentrates recessive genes into the progeny and homogenizes the genetic pool which results in propagation of genetic diseases across successive generations. Lowers fertility or impacts survivability or decreases viability of pregnancies (resulting typically in miscarriages).
Even without the incest consideration, it would be a good idea for game play reasons to implement recessive traits (positive, negative, and neutral recessive traits) such that in general inbreeding between monsters with recessive traits would be discouraged and suboptimal, and some of the other wise game breaking traits can be strictly recessive traits which would make their acquisition and retention across generations harder.
A basic example of a recessive trait would be say a "Sterile" genetic trait which doesn't become active if only one copy is inherited both parents, but becomes active if two copies of the same trait are inherited one from each parent. This creates classes of characters that are carriers without expression, are carriers and express the effects of the trait, and characters that neither carry nor express the trait.
While I'm on the topic, consider the possibility that some monsters might require or benefit from more than one other mate; one-on-one should obviously be basic, but there is opportunity to develop different reproductive game mechanics inspired by real world reproductive biology. One example might be
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like ants or bees, or
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like in some reptiles.