Instead of bisecting the top layer with roads and fences, build all major roads in tunnels, and bring the recovered surface area back to it's original state for all to enjoy.
Availability of suitable habitat for native species is only getting worse. If we blindly follow the path we are on, confrontation and compromise are inevitable, and humans don't typically lose this battle.
It's no surprise city centers and golf courses occupy the most desirable land (valleys along waterways). Southern California especially has a habit of teraforming natural waterways and fencing them to prevent access; it's amazing any water is still available to wild animals.