Not taking into accounts the awards, championship, and accolades (which obviously Jordan has over Lebron at this point) here are my comparison of the two. Note that I'm taking the pre-retirement version of Jordan (his first stint with the Bulls) because he lost a step even after his first retirement.
Overall Scoring: Jordan by a considerable margin. Jordan played in an era of handchecking and the flagrant fouls they call today would be regular playoff fouls back then. Even so he scored more at a higher FG percentage then Lebron both in the playoffs and regular season.
Long range shooting: Jordan by a slight margin. Forget the 3 point shooting percentage (more or less a wash or slight edge to Lebron), the NBA 3 point line was much further in Jordan's era. If the in his prime Jordan has the 3 point line of today, he'll probably shoot almost 40% on his threes. That said Lebron has improved and when he's hot, he's very hot from downtown.
Medium range shooting: Jordan by a large margin. Lebron has improved a lot (especially when he's going left to right and shooting from his "sweet spot), but Jordan was one of the best mid range shooters in history; almost as good as Dirk is once he was acclimated to his fadaway jumper. His shooting percentage will attest to that (over 50% almost every regular season and post season in his prime). How often does Lebron shoot over 50% in an entire regular season or post season? Granted, perimeter players are more athletic today but the rules favors offense more and there's a dearth of great centers. Plus the eye test. Lebron generally look slightly awkward on his jumpers while Jordan's shot just looks much smoother.
Dunks and layops. Tie. Lebron is considerably taller and stronger than Jordan. Lebron probably can jump slightly higher (because of his height). Jordan certainly have the advantage in hang time and body control in the air. Jordan looks more graceful in the air and makes more difficult, contorting shots, but Lebron's height allows him to finish over tall centers easier than Jordan.
Fast Break offense: Lebron by a moderate level. Even more so than Magic, Lebron is the best fast break specimen of all time. His height and vision makes him impossible to stop. His speed and athleticism makes his dunks or layups next to imposible to block. If their is a stat on shooting percentage in the broken floor, Lebron might be the most efficient ever. Jordan of course is no joke but he's not as good a passer in the broken court and his height may not allow him to finish with quite the regularity of James (even though that aspect is close because of Jordan's legendary hops).
Fast Break defense: Lebron by a slight level. Jordan has very fast hands and excellent lateral quickness (as he showed defending against a 3on 1 fast break in a famous playoff game). However Lebron's height and his presence as well as reputation for coming up with blocks trailing the breaks often alters shots and intimidate players (like Derreck Rose a few times).
One on one defense: Jordan by a slight to moderate margin. Lebron has improved in this regards immensely (Derreck Rose found out). However make no mistake, a young Jordan is the best one on one perimeter defender ever. Everything Lebron did against Rose, a young Jordan can do also. He's quicker and has faster hands than Lebron. Lebron is taller but Jordan was an expert at blocking/ contesting shots in a one on one situation also. Many people see Lebron dominate Rose one one one. Rose is too young with a limited offensive moves and questionable jump shot. Those qualities (along with his height disadvantage) would make him easy picking for tall, athletic wings like Jordan, Lebron, or Scottie Pippen. He cleared space a few times against Lebron but can't make his jump shot. To become totally unstopable, Rose must develop his mid range jumper and add a few more offensive maneuvers to his arsenal.
Help/Team Defense: Tie Lebron is vastly underrated in this respect. The eye test will show just how much better the Heat are defensively with Lebron on the court. His height and athleticism makes him a constant threat to block shots from the weak side. Trust me this alters shots (as it did multiple times with Rose's layups). Jordan advantage is his awesome rotations and alert ball strips (2-3 steals a game in his prime). He's also less likely than Lebron to roam and is more contained than Lebron.
Pick and Roll Defense: Jordan by a slight to moderate margin. Jordan was an elite pick and roll defender (one of the hardest defensive skills to master). He fights his way through screens very well and uses his excellent lateral quickness and hands to disrupt both shots and passes. Lebron's height and athleticism however compensate for much of his tendency to get lost in certain pick and roll situation. His blocking ability often allows him to contest/block shots he have no business contesting.
Passing: Lebron by a moderate level. Jordan was underated as a passer (remember the finals against Magic in which he averaged almost 10 assists a game?), however Lebron is probably the best non point guard passer in league history. This versatility may be the reason Pippen stated Bron as the best overall player.
Rebounding: Lebron by a moderate level. Jordan was among the best rebounding 2s but Lebron's height and power makes him the superior rebounder by a decent margin.
Ball handling. Lebron by slight margin. Lebron's ambidexious nature gives him arguably the best off hand handle in league history. His height also allow him to look over the top of almost any defender. Jordan's large hands also gives him excellent handle and in his prime, he can score efficiently no matter which direction his defenders forced him.
Clutch scoring. Jordan by a considerable margin. Lebron's athleticism and streakiness makes him a terror in the clutch but his off balance jumpers are oftentimes unpredictible and unreliable. Jordan's amazing mid range game makes him impossible to guard with any degree of confidence. He seems capable of unleashing a 50% shot whenever he wants, which is an extrememly high percentage in the end game.
Free Throws: Jordan by a moderate margin. Look at stats. No explanation required
Intangibles. Jordan by a considerable margin. Jordan's killer insticts is truely remarkable. He never had a bad playoff series. That is truely remarkable because Kobe, Lebron, and now Rose have all have had terrible playoff serie(s) in their careers.
Athleticism: Lebron by a very slight margin. Jordan's faster(small margin), quicker laterally (moderate margin), have better body control, and have superior hang time. Lebron can jump highter, stronger, "looks" more athletic, and is almost as fast as Jordan. Lebron's size/strenght/speed ratio tips the scale ever so slightly to Lebron's favor but an in his prime Jordan was one of the most graceful athlete of all time.
In short Lebron certainly have the potential to surpass Jordan. If he ever develop a consistent jumper he'll be
much more reliable in the clutch. His height/speed/athleticism combo is unprecedented in league history but he must learn to shore up his remaining weaknesses.