...pieces that are brilliant, or at least very good, overall.... but possess a flaw, or a quality you don't like at some point in the piece.
Prokofiev, piano sonata #7, the beginning of movement 2. The melody is mediocre at best, and the rhythm isn't so hot, either.
Prokofiev, piano sonata #4, andante assai movement. While I don't really know the entire sonata well, I know this movement well because I have a recording of Prokofiev playing it. It has some wonderful parts, but they are put together stupidly.
Brahms, piano concerto #2. There is a terribly jarring transition in one of the movements. I'll have to listen to it again so I can note the exact place. While, for me, Brahms usually bores or grates, this piece was played brilliantly by Artur Rubinstein in a live recording in Warsaw, 1960.
I don't like the second movement of Beethoven's Op. 110, although I don't much care for the entire piece, so perhaps it shouldn't be part of this list.
The climax at the end of the first movement of the Scriabin concerto can be overdone to the point of annoyance. The otherwise perfect Ashkenazy/Maazel recording blasts it.
The noise blast at the beginning of the final version of Rachmaninov's 4th concerto, probably designed to make the concerto more "hard"/"masculine", doesn't add anything of value.
The last movement of Prokofiev's 6th symphony is regrettable, at least judging by the recording I have which has two wonderful preceeding movements.
Some of Bach's organ pieces irritate me because they are minor throughout and end with a major chord. It's not always satisfying. If I were playing them, I'd change the ending chord in such instances.