You're right, the second-chance premise has a lot of potential. Possibly more than Roddenberry's wagon train to the stars.

Roddenberry was pretty relentlessly upbeat, and I think that that limited his scope for drama. If humanity was good and successful and expanding and assimiliting species into the Federation faster than the Borg, then dramatic tension had to come from opposition to the Federation. Opposing the Federation had to be inherently evil, and with humanity already cast in the good role, aliens we assimilated were good, and aliens outside the Federation were simply evil.

The Greeks are said to have defined tragedy not as good versus evil, but good versus good. Roddenberry's premise allowed only good v. evil, but the second-chance scenario has a lot of good v. good potential. Especially when we're fleeing a disaster of our own making, as in the ecological collapse scenarios like TN. Then the writers can play with the moral issue of whether we deserve a second chance, and the factions can be philosophical rather than commercial.

Is it gooder to build the colony to ensure humanity's survival, or gooder to let evolution play out and let humanity pay the ultimate price for its sins?

Meat. Give me more meat.