I don't understand the "lack of respect" thing. I really don't (other than Wolverine, who obviously doesn't like him that much at first). At least when I look at how the character is actually portrayed.
I get that he didn't have a ton of screentime, and that he, well, died, but Cyclops was still portrayed very well and rather faithfully in all three films. There's a precedent for his behavior in all three films somewhere in his classic characterization.
The X-Men were more or less treated like an ensemble, and still are, in this franchise.
When Scott was "sidelined" in X2, much like the comics, it was because the plot required the less prepared X-Men to band together without their leadership. It was done for a reason. And even then, his interactions with Jean were fantastic, as was the finale between them, and he and Logan, etc.
What we didn't see, and haven't seen in the franchise, was Scott developing from a troubled, unsure young man into the confident battle-hardened leader he more or less already was in X-MEN. I'm sure we'll see that in APOCALYPSE, with the recruitment of Scott, Jean, Storm, etc.