I think that there is a world of difference between analysis of music and using analysis to create new music meaningful to human beings. The acid test is surely to attempt to devise an algorithm, for instance by writing a computer programme, to create music meaningful, in some original sense of the word, to the human listener. Since music, it seems to me, transmits its meaning mostly by semantic association rather than by syntax, the task is very difficult. Sure, several people have succeeded in writing programmes to analyse and compose music in traditional styles - David Cope is the most remarkable, you can download a couple of examples from his website - but there is a world of difference between these extremely clever stylistic imitations and producing something with a spark of originality and surprise.
Rhythm ? Far less susceptible to analysis than harmony surely. For one thing rhythm exists in continuous time, not as a set of discrete pitches and their distributions like notes and chords. If you restrict yourself to metrical, notated rhythms, such as in a fairly regular classical piece then, give or take a couple of speed changes you might be able to represent rhythms as, for example, chunks of binary zeros and ones.
10010010 for a rhumba - you know what I mean. Even then, as I found to my surprise the last time I wrote a composition algorithm, accents still need specifying, or else the ear perceives most things in twos and fours rather than threes. Even in the very simple rhumba above, the effect is markedly different depending on which 1 is accented.
So overall, I am inclined to agree with you that rhythm and phrasing are still the elements yielding least readily to analysis.