Jordan's a better shooter? Of course Jordan shot a better % from the field because Kobe's attempted 2,051 more three pointers than Jordan did in his career -- three pointers are, by nature, a lower percentage shot. And naturally that's going to bring his shooting percentage down as well. A much better indicator would be points per field goal attempt, where Jordan does have an advantage so slight it's silly to hold it against kobe. Kobe was better from three, as you mentioned, and if you don't think Kobe has a great mid-range game you clearly haven't been watching him play. It has also been said that Kobe, having worked with Hakeem Olajuwon, has one of the best post up games of any guard ever. Free throws are even.
Jordan's a better leader? He punched Steve Kerr and Will Perdue in practice, ran Doug Collins out of town because Collins wanted a more team-oriented approach, called Kwame Brown a "flaming faggot" when Brown was just out of High School (and drafted by Jordan, hm...), and there has to be more than that -- that's without even mentioning the secret suspension for gambling. Kobe "ran" Shaq out of town, but considering Shaq's had bad breakups with every team since leaving the Lakers, it's beginning to look less and less like Kobe's fault.
Jordan turned the ball over less? Kobe's averaged 2.9 per game, Jordan averaged 2.7. What an overwhelming margin...
Jordan's a better defender? Kobe, like Jordan, is an annual fixture on the first team all-defensive team. Jordan was great, don't get me wrong, but Pippen was the better defender of the two and is the one who typically defended the opposing teams best player. Jordan had more steals per game than Kobe, but so did Allen Iverson and he wasn't much of a defensive presence, was he? Kobe also plays in an era where you can't hand check opponents and aren't allowed to be as physical.
For assists, in their primes the numbers are about equal. Kobe's career numbers in all categories are hindered a bit by the fact that he entered the league as an 18 year old.
Yeah, the eras aren't so different, but not counting Jordan's stint with the Wizards, Kobe was 18 and 19 years old in Jordan's last two years. The game has actually changed a bit since then. As I said, more complicated defenses, bigger, stronger, faster players.
By the way, win shares is a pretty worthless stat in basketball.