Star Trek is about optimism for our future, in that we have evolved past our self-destructive ways, embraced difference and are on a 'quest' to better humanity. But that doesn't mean that they can't deal with dark and very real issues (in a sci-fi context), showing how the characters over come adversary (or possibly how they are consumed by it, only to rise from the ashes).
There is always hope, no matter how bad things may be, how bleak the immediate future looks. Trek should never shy away from tough issues and things that might cause controversy because the PTB want to 'play it safe', especially after they mediocrity that was VOY and ENT.
Have darker, grittier episodes, story arcs, character development, but I'm not sure an entire series would work that way without becoming depressing.