It IS a superhero movie, but the X-Men, in particular Logan and his Weapon X stories, are a different breed of superhero.
The X-Men stories aren't your typical "duh duh duh duh!!!" "I'm a superhero! I fight evil super powered criminals to save the city!" type of superheroes.
I almost see X-Men as more fantasy - these are people with evolved capabilities, and there are particular conflicts that they face and must fight again, but it's not your typical Spiderman style masked hero saves the day with headlines in the Daily Bugle, and alternate identities to protect Peter Parker.
There's political relevance, the issue of bigotry and the struggle for equality. In the past, it's been women, blacks, Jews, native Americans, etc... fighting for their equality, these days it's the homo-sexuals. It's a theme that is timeless.
It also has many shades of gray. Magneto isn't evil. He may be misguided, but his intentions are honorable. Some of the heroes are exactly selfless individuals who act nobly to protect others. A character like Gambit - he's not exactly a "hero". Sure, he may do the right thing, but he'll also do the wrong thing if it personally benefits him.
These characters also aren't flawless individuals. They are 3 dimensional. These things that give them great strength are also great weaknesses. These characters are human - with human strengths and weaknesses, emotions, flaws.
There's just so much about X-Men that I find to be so much deeper than anything else out there in regards to comics and superheroes. And hell, a lot of fantasy and fiction in general.