I don't get the idea that the Trek universe has become "very dark." Yes, some bad things have happened, but there are good things happening as well. The Cardassians and Ferengi are now solid Federation allies, the Romulan government is as benevolent and progressive as it's ever been, slipstream is opening new vistas of exploration, the DTI helped bring a major chapter of the Temporal Cold War to a close, and so on. While on a personal level, both Picard & Crusher and Riker & Troi are happily raising children, a number of formerly divided DS9 characters have been reunited, many VGR characters have overcome serious personal problems and are now in a better place emotionally, others are healing from the scars of the Borg Invasion and moving on with their careers and relationships, etc.
And it's not like previous Trek series were devoid of their darker moments. Just look at TOS. Kirk repeatedly suffered the deaths of family members and lovers, and was the survivor of an act of genocide in his childhood. Whole planetary populations in the billions were exterminated by Nomad, the Doomsday Machine, the neural parasites, etc. War broke out with the Klingons and was only stopped by the heavy hand of the Organians, and after that an ongoing cold war played out. Outposts were destroyed in border conflicts. Penal colonies fell under the control of madmen and torturers. Miners unknowingly slaughtered thousands of unborn alien children. Enterprise
crewmembers died by the handful, and whole starship crews were exterminated on multiple occasions.
And yet, despite all of that violence and death and grief, TOS is considered an optimistic show. So why this perception that there's nothing positive happening in the books today?