Good question, I've been thinking about it lately. This would be my top four:
No complete strikers - hence poor conversion rate meaning lots of chances need to be created (part of the reason we seem to "start slow").
Lots of chances need to be created to get a lead. Whole team working harder and moving more, lack of emphasis on defending for longer periods. Therefore we tend to concede in matches when we don't take the lead early - most of them.
Defensive errors, especially by centre backs. Ours - particularly Vermaelen - have been mistake prone in pressure matches. Enough said.
Deficit of strength and ball-winning ability in what would otherwise be our best midfield. Has been better since Ramsey came into his own a bit.
All of the above are why we sometimes seem like a team optimised for hammering crappy defences. When we face disorganised sides, we score early and every aspect of the game then improves for us.
Top level strikers are definitely the big difference between us and the incumbent champions, but any idiot could tell you that.