Could anyone explain to me how the score doesn't fit into the PT movies? Or some examples of flaws / hackneyed work?

I believe to have paid enough attention to this stuff when I used to watch these movies, and it always came off rather well to me.

(The "arena" track that you can also hear on the Clones DVD menu, has been replaced by the AniPad love theme, and inserted into the Evil Jedi Temple march in ROTS instead; given how awful the romantic scene preceding the monster fight was, and how this track doesn't sound evil enough for the scene it was eventually inserted into, I'd say overall it wasn't the smartest decision, but it didn't seem awful or disturbing or anything like that.
The music that hits in when the Jedis arrive has been taken from the Podrace (which instead used the same track from the Nubians' "shield crisis"), but fits pretty well anyway.

At any rate, there's some awkward "copy&paste" thing going on in the PT, but never to a level of badness imo.

The only part I didn't like was the Conveyer Belt that kept jumping between the eponymous track, the Force them and AniPad. It was bearable, though.)