Okay, why must people always break it down to 1-on-1 fights.  That's drastically unrealistic.
1) Flash beats the entirety of the weaker X-Men while the group is still figuring out that there's an opponent, leaving Jean and Charles. Assuming we aren't attributing the Flash his maximum powers, Flash and Superman beat the entirety of the weaker X-Men while the group is still figuring out there's an opponent. This is all assuming the JLA are acting stupid and saying, "Gee, they brought a guy in a wheel-chair to the fight...I sure hope he's not some sort of hidden psychic (or, mystic, would be another reasonable suspicion, albeit an incorrect one) powerhouse. Ah, well, let's attack the ones we can easily smack aside with a thought first." If we are not attributing extreme stupidity to the JLA, the fight is Jean v. JLA.
2) The JLA are one of the best "Team-work" teams there are. Ever. The X-Men are fractured and often lack trust in each other. They work together okay, unless they're in one of the BILLIONS of times of inner-turmoil those little angst-pots go through each day, apparently.
3) Phoenix would do a lot to equalize this battle. If the X-Men had Phoenix, the JLA would have someone they would actually have slight difficulty taking down. Without Phoenix, this fight is over within seconds. With Phoenix, I would attribute to the X-Men a 1 in 20 chance of victory.