There's a formatting problem here. How many speakers are there and who says what? In the first triad, John could mean "It's terrible because it doesn't make any sense", but the first speaker couldn't be saying the third sentence. What doesn't make any sense, John's "I think that sucks!" response or what the speaker has asked John to comment on? Irene's suggestion that "It doesn't make any sense" sounds as if it might have come from a third speaker is a good one. It does to me too.
In the second triad, The first speaker seems to be making an ad hominem attack on John because "You're not making any sense" is about John and what John says, not about what the first speaker has asked John to comment on, which requires "It doesn't make any sense".
First, the dialog needs to be clearer, which means that the names of the speakers (even if only "A" and "B") must be included. Second, there is no context for the first line that asks "What do you think?" What does John think of what? Maybe the pronoun "that" or "this" is required (minimal context but no change in meaning). To understand why John isn't making any sense, we need to know what he's been asked to comment on and why his "I think that sucks!" response is, apparently, inappropriate.
There is no change in emphasis from the first to the second triad, only a change in focus to from either what John says or what John has been asked to comment on (it) to John himself (you're).
In other words, without more information, this question cannot be satisfactorily answered.