(1) The A and B plot may have been an innovation compared to Star Trek
, but it was hardly remarkable in terms of dramatic television in 1987.
(2) Star Trek: The Next Generation
definitely took greater narrative risks than its predecessor. As you've pointed out, character arcs developed over time, secondary characters were highlighted on a recurring basis, etc. Nonetheless, compared to dramatic television in 1987-94, I'd hesitate to call any of this truly "innovative," although unlike VOY or ENT, it was at least keeping abreast of changes to television.
(3) I'd agree that TNG is "genuine sci-fi" (although I'd drop "genuine" as being redundant; it's either sci-fi or it isn't), but I'd also argue that the later series were just as much science fiction as much as TNG was.
(4) I (shockingly!) disagree with your assessment of the Abrams movies as lacking any distinguishable elements of STAR TREK. To my eyes, they get as close to the original series as anything in their sense of adventure, pace, aesthetic, and tone.