I think you're forgetting how integral he was to some key plot points in early 2000's X-Men stories, not to mention that he's still a super popular character with a movie in the works.
Just because he isn't relevant now doesn't mean he isn't relevant ever.
Smooth Criminal
Oh, right that movie. The movie that has lots a bunch of directors, producers, screenwriters, in development hell, has a really popular Hollywood star attached that will eventually leave it too, because it's taking too long to make, and he'll eventually not have the time for it? Thus effectively killing it?
That movie isn't happening ever.
16 years ago is still a long time away. He can't hold a solo book (in fact this is true too at the height of his popularity as well), he's never been a huge seller for Marvel on his own, each attempt lately to revitalize him has failed.
My point still stands. Gambit simply does not matter to the current Marvel or X-Men slate and thus he's not a necessary component anymore to represent either Marvel or the X-Men.
And I'm not saying this to hate on the character, because while he's not one of my favorites, he definitely has some solid and interesting merits as a character, there are just people who I'd rather see in a Marvel crossover/X-Men game than him at this point.
I'd be saying the same thing with Eddie Brock Venom. People always cry for him, but he hasn't been Venom in such a very very very long time.