What I have in mind is excatly what Oberlus said. There should be two factors: Number of species AND how they are distributed. That means plantbound species does have a great impact early on with few colonies but it get less as more colonies you have. That means you really have to decide if you capture a native species or keep them. At the moment it's often you just capture them because of the +0.5 stability, not for the output (PP, RP, good ships etc)Currently it works the same for planetbound that for other species. With this, planetbound would be less interesting, but they would still contribute to number of species, which (as currently) would be considered.
I had that once. Get Eaxaw late on and could compensate the -12 xenophob malus on stability with +16 from diversity. That somehow felt wrong, because the policy eaxaw hate mad them keep calm...Really ? That means 28 to 34 Species in your Empire, quite impressive to get that early enough to make a difference...
I never encountered such a situation, I'm lucky if I get +5 from it.
At the moment I play with low natives and get 3 - 5 stability out of diversity. That feels much less overpowered.
Edit:
With the changes in influence (Artisan lowered to +2 and good influence lowered to 125%) it doesn't feel out-competing for me. I think it's quite balanced. On the other hand, wide Empires are always better than tall, but I work on that to address it in my kosymod.I'd say it's more the combination Diversity+Artisan Workshop that is out-competing