Naruto is not lacking in leadership any more than anyone else. I'll try to make it clear why I think this. In the forest of death, sasuke is the one that came up with the plan that would prevent other people from infiltrating the group when he came up with that long password that Naruto would never remember. Point for Sasuke because he's thinking ahead. Nothing else that involved ledership comes to mind about Sasuke. The other genins, other than shikamaru, haven't really shown any more than Sasuke has (even though you may assume they did)

Naruto on the other hand, motivated Sasuke to go from sissy to badass against Orochimaru. He then came up with the plan to defeat the three ninjas who used the replications. Talking about leadership qualities, motivating your troops is as important as anything else, and being able to do that is a leader's quality. Naruto has it innately and it doesn't matter what exactly it is that gives him that quality.

Combat strategy and tactics are also as important as anything else. To be able to come up with an effective combat plan, you have to possess a good degree of foresight. Naruto, time after time, has come up with combat strategies that made the difference.

As far as "finishing the mission but getting all your troops killed isn't good enough...blah blah..." Naruto has that covered as well. Those goop ninjas. Not only was the plan his, but he defeated them alone, leaving the rest of his team unharmed. Hell, they weren't even tired. As far as the people deciding who has leadership abilities, it seems to me that you can't use the third exam as the guage. A one on one fight is not the same as a team battle or a team mission. You're not worried about protecting your troops, because they're not a part of it.

To make it worse, their judgement was mistaken, because neither naruto nor neiji had a reason to give up on the fight. Naruto has a demon in him that he know how to use, and neiji dominated the fight until naruto pulled out that demon. Was naruto supposed to give up before pulling his trump card? Was neiji suppose to give up before seeing what the demon could do? NO! dammit!

It seems to me like you guys are making your judgement calls based on the overall feeling you get from the characters as opposed to what they've actually shown. If anyone has a counter argument I welcome it (not trying to get into a fight), but please make sure you can topple the things I just stated instead of just posting and leaving everything I said still standing, otherwise, this goes nowhere.