From what little I know of Destiny (basically just the overall storyline), the comparison to NJO is an obvious one to make. However, I suspect Destiny will end up being the stronger story overall since it is a trilogy and won't be dragged out over 19 goddamn novels - seriously, no single storyline warrants that many books. Plus, it looks like Star Trek novels will be reeling from the effects of this story years later, whereas aside from a Vong-formed Coruscant, you could easily forget the Yuuzhan Vong war ever occurred by the time of the Legacy of the Force novels. Star Wars books just jumped ahead like 10 years in the narrative. It'll be interesting to see what the Trek universe is like a month or two after Destiny, should Destiny really bring about the huge changes some have speculated it will.
I'm sure there will be other differences between the stories, and seriously, the story of the more powerful enemy coming to conquer all in their path is just sort of staple of the genre...Hell, not even the genre, just storytelling and history itself.