You guys are forgetting how ridiculously powerful telepaths are in Marvel. The X-men do have that advantage working to their side when fighting the JLA. Phoenix, Phoenix II/Marvel Girl aka Rachel, Professor X, White Queen, Cable with his virus in check uber powerful, etc...They could turn off a lot of the weaker JLA members brains easily (I'm not calling Batman weak, but if the X-men hit him with a telepathic assault it's endgame for him), and the others not so easily.
Not to mention that Iceman is one of the most powerful mutants in Marvel right now, and he's still not as good as he could be. I've seen him litterally freeze someone's blood with just a thought, absorb a river to become a giant. Use your imagination, there are plenty of icey ways to die.
Lorna has been upgraded in power. She may be a poor man's Magneto, but even then she is still a very formidable force.
If Batman brings any electrical equipment Shadowcat will screw it up. She'd be the hardest to hit. I do not know who could hit her unless she was taken by surprise it'd have to be a mental assault.
Storm can make things miserable for any enemy as long she keeps a safe distance.
The X-men fight very well as a team, especially when Cyclops is on the battlefield.
However, if JLA surprises X-men i'd see them winning easily from the speed advantage. If X-men, surprise the JLA then I think their telepathic capabilities are too overpowering. The X-men would win easily.
I admit I know a lot more about the X-men than I do about the JLA, but i'd still give the X-men a fighting chance. I think it could go either way if each side knows the fight is coming. That'd give the X-men enough time to get all their little shields and the telekinetic things ready for the onslaught of JLA speed.
With prep time? Well, the X-men don't really use a lot of machinery, they rely on their powers mostly. So i'm inclined to think the JLA takes it with prep time and knowledge of the others.