It's a bad system; it promotes upvoting the already top-comment and commenting on it or the initial replies to it; the best way would be to pseudo-randomize posts order but biased towards those with higher score (e.g. so the top-rated-comment sometimes appears second, some rare times third; and some extremely rare times forth [regardless of how old any of those comments are])
An option to hide/expand comment trees might help, as you could easily hide the first comment (and everything that hangs off it) and check out the next ones (without having to manually scan indentation).
