I think the subreddits should only be created after enough articles for given category were posted (and upvoted).

Agreed. This is why I shut off main and forced everything into discussion--I don't think we know enough about how LW will be used to partition things ahead of time. (I'm also pretty skeptical of doing a subreddit split on topics instead of on rules.)

Upvoting and downvoting should be limited to users already having some karma; not sure about exact numbers, but I would start with e.g. 100 for upvoting, and 200 or 300 for downvoting. This would prevent the most simple ways to game the system, which in its current form is insanely fragile -- a single dedicated person could destroy the whole website literally in an afternoon even without scripting. This is especially dangerous considering how much time it takes to fix even the smallest problems here.

Currently the limits are 10 for both upvoting and downvoting. We've already seen some innocent bystanders hit.

I think you're underestimating the difficulty in getting up to 100 karma. (One comment made a while ago is that the fragility of the voting system--especially when it comes to serial downvoters--happens in part because of how infrequently good users vote. It is problematic when we exclude people with good taste who don't contribute much, because that means the base of good votes to overcome is even shallower.)