I do the opposite of you, Nightingale. If you're breeding for battling, every -% is a loss in total stats, while every +% is a gain. I put no points in the decreased stat, and max out it's complementaries as much as possible. These are in the faq somewhere, for example, STR + COURAGE = Damage, (0 + 60) is the same as (30 + 30). Now if you put 0 into STR, you're going to be squishy because defence also depends STR and CON. So then you shift around some points to fix the deficiency.
Max Str, Int, and Intuition (1 in rest) gives the same result as 3 in everything, which gives the same as max Agi, Courage, Con (1 in rest). Also you can choose to boost four stats to 4 stars, and leave the other two low - as long as the two you decrease aren't complements. It'll make your pet weaker in certain aspects, but the weakness is spread out as much as possible. This way you can boost things you want (like + dodge to increase effect of dodge genes). Just find some combination that supports your pet's genes.
If all stats are normal, default setup is good so that the pet can do all your crafting/building/questing needs.
Recent progress: Project Perfect