Making Trek just dark would obviously be heresy,
Nah, TOS was pretty dark at times when you remember that in the show a planet with billions of people could be snuffed out at any moment from either doomsday weapons, or space monsters, or bored godlike beings.
Not to mention all the energy being or other aliens who use people as meat puppets or just plain toys for their own twisted amusement.
Then there are the things that literally suck the life out of people.
Also the fact that the universe will explode if two guys locked in mortal combat ever both show up in the universe.
Not to mention the the Federation was always pretty close to war with the Klingons which is usually describe as something that would be devastating.
Oh and if your in Starfleet and assigned to a ship that is not the Enterprise chances are you will die a horrible death in the empty void of space. And even if you are on the Enterprise chances are the first time you visit an alien planet you will die and in some cases quiet horribly.
Then there's the fact that everyone is one trip to the galactic barrier away from dealing with a rampaging mad god.
Seriously all the show needs at this point to go totally Lovecraft is the appearance of godlike aliens who either drive you mad or mutate you. Which were probably hiding on some rock out there somewhere.
So what was that about Star Trek being a Utopia again?
When people talk about darkness they do not refer to the horrible situations the people of the Federation might find themselves in but their basic attitude which is, as Sindatur has pointed out, neither depressed, cynical or desperate.
Thats because nobody has really given a though to the type of world they live in.
Or they're on something, I mean the people in the future don't feel grief thing makes me think they were on something.
Not to mention how after a situation where billions died Kirk and co. were doing a happy jokey ending.