This well known masterpiece is a wonderful mix of passion,
deep structural rigour and, at the same time, bloomy
ornamentation (in the fugue). I don't think there is any
particular one way of playing it the "right way". I also
think few organists will play it twice in the same way.
One further observation: The fugue ends with a threefold
repetition of the theme in the pedal. I remember to have read
somewhere that this is a unique feature in Bach's compositions.
However, the same also appears in BWV 589 (Alla Breve in D) between
Bar 32-44 (starting in alto). Bach's authorship of
BWV 544 is undisputed, with existing autographs, whereas there
have been doubts about BWV 589. In my view those doubts
are unfounded, judging the harmonic style and structural
maturity of "Alla Breve". The similarity with BMV 544 in the
particular feature mentioned above may add evidence towards the
true authorship by Bach for BWV 589.