First of all, I find it cool that you guys are discussing things from my guide xD Quite a compliment in itself if you ask me, so thanks a lot!
Anyway, Doodle, you can't really compare those two pets - the first one has inherently 10 additional points to ALL their stats from being GP1, meaning they will be stronger than the other one, no matter what. And that is a big difference. Considering that monsters on islands never have GP (except Temple Guardians), your pet will be automatically better than most "normal" pets and more likely win.
Also, I never actually said to boost all the "top stats" and ignore the worse ones. What I did say was that you should boost the GREEN stats (meaning ones boosted by a gene) because you get more out of them, like if you have Quickmind, which gives you 50% additional Intelligence, you basically get 1.5 points every time the game assigns a point to Intelligence. Say if you have a lvl 1 pet with 30 base Intelligence and Quickmind, even at this point it already shows 45 Intelligence (30 base + 50% = 45). Now if you managed to get only one point for every level on this pet, at level 50, the base Int would be 80 (30 + 50 levels*) - and again you would get the 50% bonus from Quickmind, resulting in 120 Int! (80 + 50% = 120). Now if you set the corresponding food for Int to 5 stars, you might actually get quite a few more points per level than 1!
Take the opposite example: A pet with Silly has an inherent -50% on Intelligence. Let's assume our level 1 has the same base 30 Int. Because of Silly it will only show up as 15 Int! (30-50%=15) Now let's assume you don't change stats and your pet gets 1 stat point for each level, ending with 80 Intelligence again (like in the last example) - because of Silly the pet actually only has 40!!! Intelligence now (again 80 - 50% = 40).
So if you do what some people do and try to boost this stat, can you see how many points you're wasting, still not getting far?
So what makes sense is to boost the green stats that get a bonus and ignore the red stats that only "swallow" assigned points.
I generally leave settings on pets with black stats as they are, since the few points difference in the end don't make that much difference in my opinion. At most I would move the stars for Strength to full so I get more breedings. However, if you do want to change something there, my personal opinion would be to boost Strength, Intuition and Intelligence, because with those three you still influence all the battle stats:
See how with Str, Intu and Int you still have one good stat for each of the battlestats? Strength affects Defence and Damage. With Intelligence you get Accuracy and Anti-Crit and with Intuition you are covered on Dodge and Crit Chance.
I have never actually tested anything with this, it's barely my theory that this should work well. It would be rather interesting to level a perfectly "Normal" pet with this and see how it does, what do you think?
* Umm actually it would be 30+49, since you are lvl 1 already and only get 49 levels until you reach 50.. But it's so much easier to calculate with 50 that I left it at that ;-)
Thanks for sticking around this long, I know this turned into a short novel here....
Also on a side-note: Do you think adding this to the guide would make sense? It seems rather long-winded for a new player, but if you feel it would make this whole topic clearer I could certainly put it in.