To follow the movies a bit more and make things a bit simpler, I'm going to remove some members from the X team:
Cyclops
Rogue
Professor X
There are still more people on the X3 team compared to F4 team:
Movie X-Men (x3)
Storm
wolverine
Iceman
Shadowcat
Colossus
Angel
Movie Fantastic 4
The Thing
Mister Fantastic
Invisible Girl
Human Torch
However, the X3 team is a bit inexperience, except for Storm and Wolvie.
Human Torch can burn as hot as the sun and I think Wolverine can be fried faster than he can heal - it might not totaly kill him, but it would damage him severely for a period of time.
I think The Thing is stronger than Colossus. I have yet seen Colossus match his strength to The Thing - the guy stopped a truck. In terms of invulnerability, Colossus might come up tops and in the movie he can protect another person in his metal form. So, this comes in handy for team defence.
Iceman fighting Human Torch: Iceman would vaporise - considering the fact that Human Torch can fry earth's atmosphere (according to the movie). This might be a long fight though as I think Iceman is smarter and calmer than Torch. Taking this into account, Iceman might win, if he knows tactics and uses his environment.
Shadowcat versus Mister Fantastic: Shadowcat wins, because she can phase Mister Fantastic into a wall or ground and he wouldn't be able to do a thing. However, if Mister Fantastic did know Shadowcat's abilities, he might win by early preparation. So, he might invent some gadget to neutralise her skills.
Storm versus Invisible Girl: This one, I'm not so sure. Storm can do range attacks, but Sue has force field.
Things don't so look good for the X3 team, only because of the Human Torch and Mister Fantastic.
But if you add Professor X, Cyclops and Rogue, I think the X3 team might win. Again this depends if Reed knows about X's telepathic abilities. He could easily create a device to block out Charles like Magneto and his helmet.