[link to original on tumblr]
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The "better, baby" in the first line ("Good morning to you, I hope you're feeling better, baby") has an ascending melody (G A B C), which reflects the meaning of that adverb. There's an ascent to represent that optimism ("I hope") and improvement ("better").
I've written before about how - while the speaker/singer seems optimistic - there are some musical things that portend ill toward the relationship in the song (like the static bass part in the bridge [to which I can now also add the static vocal melody; it also gets stuck on a G note for a while] and the dissonant tritone [G and C#] in the a cappella sections, not to mention the lyric "Kiss and make up," which seems to indicate that the speaker/singer had some involvement in the girl's incarceration). I found some more of those.
The "home" in the line "Feels so good you're coming home soon" is sung to an A note. The song is (mostly) in G major though (where the musical "home" is a G note), so there's sort of a musical implication that the home to which the girl is going isn't the same one that the singer/speaker is talking (or singing) about. It's as if she's going to A major instead.
During the bridge (particularly during the A7 chords, so roughly for the lyrics "we used to walk" and "we used to talk"), the melody is on the off-beats, which implies that the two people walked out-of-step and that there was some friction in their talking to each other.
The "and it could be so nice" is sung in either a different key or with a lot of accidentals (it's G G F Eb F D). Because of that foreign tonality, there's a feeling of difference, which I suppose the conditional "could" also points to, but it remains that the different tonality there is because of either a different key or a lot of accidentals (implying that the girl would have to go somewhere else for it to "be so nice" or that - like the accidentals - the speaker/singer would have to change a lot).