The thing I found most odd about the scales is how one scale will be there, then will disappear for a few grades, then reappear, then... well maybe not that inconsistent, but it does seem a little odd and I can't see the logic behind some of the decisions. I don't have a syllabus right by me, but I think i remember correctly that for chromatics, for example, for grade 4 you need D and F, for grade 5 it's E and Eb... F at least seems to be harder (to me at any rate!) than the two you need for grade five! Off the top of my head I can't think of any more obvious ones, but I remember thinking that seemed a bit odd. I can see how learning E and Eb together is potentially *confusing*, but only because you may pick the wrong one under stressful exam conditions, or end up adding an extra semitone on if panicked maybe... and given how many people have problems, especially under stress, starting in the lowest few notes of the flute, I would think that in some ways D could be considered harder than either E or Eb...
I forget which minors are needed for grade 5 - I agree that Bb, G# and Eb are all among the nastiest, I know you need them for 6 but I can't remember about grade 5... But yes, some of the logic behind which are needed for which grades I do not get at all. I remember A major scaring me for quite some time even though it probably should not have done! My flute teacher commented of the grade 6 scales that they have been a bit mean by not having many or even any (I'd have to double check the list) that are relative majors/minors (is A min in there to go with C major? I can't remember...) which would make it easier to learn them logically.
Actually I think F# major (and minor) is fine once you get a handle on it, it looks really evil and then when you get to grips with it it's like "Oh! I see!" (maybe that's just me...

) B Major is
hard in two octaves, to me at any rate, mostly due to remembering the fingerings and not
panicking up there - although I KNOW them, in the middle of a scale sometimes my brain just gives out! - especially with the balance of the flute for A# and B at the top. Bb I would say was among the easier ones especially when it's a 12th at grade 5 - it doesn't go that immensely high, and only two flats to worry about - and even when it's 2 octaves, really... yes, it goes high, but the key and fingering is straightforward, and once you get to grips with venturing all the way to top Bb, it's one of the ones that makes sense and doesn't contain too many freaky fingerings or anything!