I think you can darker situations and still have a likable cast of main characters. There some things from past Star Trek shows that should be left in the past:
1. The no mourning rule: Death has to mean something in fiction, as it does in real life. Having people not mourn, makes them robot not people. Death has to be something with a real impact, not something that is dismissed right away.
2. No inter personal conflict: People are always going to have different ideas to deal with a problem, having everyone agree all the time makes it seem like Star Fleet promotes group think.
3. No more pat solutions to moral dilemmas. A moral dilemma has to be a tough choice, making the best choice in a situation. Dressing up a black and white situation as a moral dilemma is not going to work anymore.