Respectfully, you're looking in the wrong place. Docility, empathy and intelligence are byproducts of a world with plenty; we only have trouble tolerating each other when in active competition for scarce resources.
Even intelligence is (in part) subject to nurture, not nature; the real advances in our ability to think seem to coincide with our mastery of fire, and the ability to sit safely and consider our day beside an open fire in the evening.
This of course goes against the grain of your ecological 'mess' scenario, which is ALSO not a function of our genetics per se. The ecological situation today is caused by our sheer numbers, not by our attitudes, although these certainly don't help.
Want to genetically engineer humans to ensure the ecology isn't impacted again? The simplest solution is to make us less fertile. Either alter males so that they produce less sperm (or have a higher probability of being infertile, or alter females so they ovulate far less or only produce a fertile egg one in (say) 10 times.
If you really want to get creative, try something like the Vulcan Pon Phar; Men only get 'in the mood' once every 7 years or so. When you stop and think about it, that would actually go a long way to solving the docility and acceptance problems as well because males would not be constantly competitive with each other to show off, only when it's a matter of survival.