I can't really address the general state of original novel series, but Christopher Golden's Mutant Empire trilogy is well-regarded as an independent X-Men story.
They live as outcasts, hated and feared by the very humanity they protect. They are mutants, born with strange and wonderful powers that set them apart from the rest of the human race. Under the tutelage of Professor Charles Xavier, they are more than mutants. They are -- the X-Men.
Volume 1: Siege
Magento, the X-Men's oldest, deadliest foe, has taken over a top-secret government installation that houses the Sentinels, powerful mutant-hunting robots. The X-Men must fight to keep this deadly technology out of Magneto's hands. But the Acolytes, Magneto's fanatical mutant followers, stand between the X-Men and victory -- a victory quickly slipping away. For a more ruthless enemy, the US government, holds the X-Men responsible for the installation's takeover!
Volume 2: Sanctuary
Continuing the X-Men trilogy, the X-Men must face nemesis Magneto and his Acolytes once again. Meanwhile, the threat of the US government remains, prepared to point the finger on the X-Men for the takeover.
Volume 3: Salvation
Manhattan is in the hands of the evil Magneto and his Acolytes as the first step to the Mutant Empire. Half of the X-Men have been captured, and Magneto's law is enforced by an ever-growing army of mutants and the powerful robot Sentinels.
The remaining X-Men must stop Magneto by turning the reprogrammed against him and be defeating the man himself. To do that, they must join forces with the US government -- who view the X-Men as being as much of a menace as Magneto -- and with one of their oldest foes, the Juggernaut!