I personally think the difference is even though the leafs look better on paper, the reason why they're not as good as they should be is due to chemistry. And by that I mean they acquire too many players from trade/free agency and it leads to just slotting in players and hoping they produce. You need a bit of organizational development and players to break through but when majority of the players are t, you won't have much chemistry and won't succeed much. Just my take on it...Nucks have a core which has been together for a while so their leadership and experience is just superior I think.
Their offensive production has been fine until recently (although it's been bolstered by their strong powerplay for most of the season).
Frankly, it's their team defence that's been the issue. You can say all you want about shots on goal being an important stat but it's not a coincidence that the league's 8 best teams are all in the top 10 in shots allowed per game. They can't expect to stay competitive with such poor puck possession. Transition offense and great goaltending will only carry them so far.
For all the offensive talent on that team, they're lacking a dominant two-way centre that almost all of the league's best teams have (eg. Toews, Bergeron, Richards, Backes etc.). Bozak, Bolland and Kadri are good, but none of them are exceptional. Their defencemen are offensively gifted, but many of them are unreliable defensively and their depth hasn't performed to expectation (Paul Ranger and Mark Fraser have been trash).
The Leafs have talent but having the "better team" means nothing if they don't play up to their potential.