IMO the biggest problem with Reddit is that too many people downvote well-supported arguments because it goes against their belief system which really stymies the conversation. I'd like to see downvotes haves some 'cost' associated with them so they are used sparingly and on content that really deserves to be downvoted.
I don't agree with their policy that those who vote in a thread may not comment in that thread but I think a lot can still be learned from Slashdot's model.
There's always going to be a way for determined users to get around the limits, but if it can reduce the number of reflexive downvotes from most users it could still be a net win.
No the biggest problem is that for the majority of reddit users that 'weak content' is actually what they come to reddit for. It's a systemic problem with the community. The comment system works fine.