I don't agree with the OP equating TOS to TNG. They are not similar at all, aside from the one, superfluous, commonality, that both have a ship called "Enterprise."
TOS was bold in a way that TNG
wasn't. "Gene vision" applies to and lessens the quality of TNG and VOY, but not TOS.
in later years the more popular sci-fi shows are those that are dark,brooding and have deeply flawed " hero's/heroine's "
I do not see any evidence of this. What shows would you name as "popular" that are like this?
I agree with the sentiment behind your premise. I'd re-state it as: new shows that try to ape TNG and VOY's "no conflict" policy would never work. They didn't work on TNG and VOY, (despite TNG's popularity, they still do not work from a storytelling perspective), nor could they work on any other show.
However, it seems that you are implying that they should be making shows at another end of the extreme, which is not a good idea either. A hero does not have to be "dark" and "brooding" to make it a good show. In fact, most people won't watch a show like that, if that is all the hero is.
Yes, a hero should have to make tough decisions from time to time where all the choices are bad - that's good storytelling. "Dark and brooding" do not have to be linked to that on a continual basis, though.