Quatrain 3 might come right out of left field, but here's the thing: "summer's flow'r" (9) is actually a metaphor for the powerful people, so long as they keep their inner selves untainted. When the story of the flower takes a turn for the worse—showing how the flower becomes infected and gets outclassed by the "basest weed"—it can be interpreted as a cautionary tale. If the powerful people aren't careful, they could end up like that flower. One way of interpreting this would be to say that the powerful people need to keep their true selves hidden, and keep refraining from evil deeds.
Lines 9-12: This section of the poem acts is an allegory for the rest of the poem. In this case, it looks like the "summer's flow'r" stands in for the powerful people, while the "basest weed" (12) stands in for the "Others" (from line 8) who are usually subservient to the powerful people, but sometimes get the upper hand.
Line 13: Is it necessarily true that the "sweetest things" become the "sourest" because of their bad "deeds"? Like, what if there was some really, really nasty person (remember: "sweetest things" refers to people), who never did anything nice to anybody in his entire life—would that person really be less "sour" than a good person who did one or two bad things? We find it hard to believe, but maybe we're missing Shakespeare's point. Isn't he just trying to say that we feel worst when we get let down by somebody we admired, had trust in, or loved?
Line 14: As for the last line, it makes basically the same argument as line 13, though this time using the metaphor of the stinky lilies.