Jim Lee was around when Wolvie's outfit switched back to yellow/blue, if memory serves (though I remember McFarlane's craptastic Spidey comic being where that change took place). And though Wolvie was yellow/blue for most of Byrne's tenure, he actually came up with the brown outfit during one of his last X-Men issues. Don't know that Jim Lee had much influence there, unlike the pouch-o-plenty Cyclops outfit that everyone seems to love for some reason.
I like Lee's work as well, don't get me wrong, but some of those ideas were just awful (Xavier wearing a safari shirt and driving a hover car? WTF?).