There are issues with a lot of bikes out there that only come to light (and sometimes too much focus put on them) with message boards such as this.
Amen. How many new Ducatis or KTMs have I read about that don't exactly run smoothly below 4k rpm? Several Aprillias have SERIOUS fuel mapping issues. This is not an uncommon problem with motorcycles. The magazine guys like to side step the issue by saying "I didn't spend much time in that part of the rpm range...."
The EPA regs are a major part of the problem. The motorcycle has to meet some pretty goofy requirements at certain rpms and in order to meet those goals the engineers stand on their heads and mess up what is probably a perfectly smooth running map in order to get the bikes to pass. Not all bikes have the same combustion chambers, cam timing, etc. so each needs different tweaks to pass.
In general I don't find the problems with the Vee all that big a deal. A remapping solves the fueling problems very easily and can produce one of the smoothest running bikes ever. The clutch issue can be solved very easily for ~$300. Big deal, it will cost you close to $300 for a new quality chain and sprockets or a set of tires.
No bike is perfect, some are closer than others, but I've never owned a bike I didn't modify in some manner to make it better for me, just some more than others.
I rode the nice new Yamaha Super Tenere and I don't like the low speed fueling/throttle response on that bike either. CycleWorld Magazine complained about it also, so ????
I've ridden quite a few of the new ADV bikes out there and I keep thinking to myself, "gee, my old Vee is still pretty damn good". My only wants are modern suspension and brakes, both of which can be improved. I have no complaints about the engine or trans once I got them sorted out.