In my humble opinion, at THESE levels of bikes, the 'flaws' come down to personal preferences:
My busa could have lower pegs [I'm 6'1" with long legs]
I wish it were less hunched over [but it wouldn't be sporty then] but I have long arms and that helps.
um... hmmmm.... nothing else comes to mind
Only had mine 2 days and been on it once.
Seriously, I was scoping the R1 and GSXR1000 but I went Busa for a couple of reasons that did not involve genitailia size:
1) I used to have a tuned up Ninja 1000 and downgrading speed was not an option [thus R1 or GIX1K] so I was used to a heavier bike and the Busa came to mind
2) I was set to buy an R1 and discovered deep in my soul I wanted a bike that I could ride longer distances too [R1 was out - too racey and track like, gixxer was out before R1 as many testers were wrecking them with that insane power to weight ratio] Busa's ergo's were SAID to be better in that reguard and it did feel better to me having sat on all 3
3) I started reading how the R1 was a wheelie monster - again with the power/weight thing. I don't mind wheeling but not accidentaly all the time. Busa can wheelie but the weight keeps it down for better traction also
4) Wind shear - on a heavy bike at higher speeds or on highways with traffic and cross winds I think a small bike would suck [read: feel unsafe even if it was, especially to an occasional passenger]
5) At the dealer I sat on both the 1300 and the 1000 and the 1000 felt like a cheap plastic chew toy for nearly the same money. I know light=speed but side by side the Busa was a mercedes
6) one of the biggest things for me was maybe that Busa was my dreambike since I'd first gotten into cycling about 4 years ago. NEVER EVER thought I'd EVER get one but here I is!
Saved up for 1.5 years and paid cash: $9949 [total tax, paper, delvery] plus my old KAW1000 trade in at $1100. Maybe I was ripped off, I don't know or care, it was fine by me.
7) I happen to love the unique look of the bike as it reminds me of those cool cycles used in Japanimations , you know the super futuristic ones that simple don't exist? This seemed closest to that to me. The Aprilla Futura was neat for a week, but getting one and getting service would be impossible to me.
Since I seldome [read: never] ride on a race track, the R1 and GIX1000 stopped appealing to me, and the Busa encompassed NEARLY the same speed [even better on the top which I'll never see] and better long ride ergo's. Better for a passenger too should I decide for that option.
So, I feel the flaws are subject to personal preferrences. I'm sure there weird mechanical things here and there but I think ALL bikes have that as part fo a physical world.
Decide what it is you really like to do and go from there. I enjoy some novice twisties, love hammering it on a long strait and feeling like an arrow, want alot of comfort along with a little extra weight to stay nose down and wind resistant. Busa seemed to cover everything.
I don't count the accelleration compared to the 1000's as a flaw when I throw in the other parts it does better. It's all a trade off somewhere. Whatever you get, you can ALWAYS make it go even faster with extra parts.... I won't be needing any.
BTW I thought your english was perfect.