[Winder]

Had an SV for 40k miles. Had upgraded rear shock, lower pegs, bar conversion, tall screen gel seat and loads of other stuff that's not really relevant to your question.
Now have a 2007 fz6 s2 and have done 12k miles on it so far, commuting and touring.
Only modification is chucked the standard bars and put slightly wider renthals on.

I would have the SV back in a heart beat.
The Fazer is comfortable but no more comfortable than the tweaked SV.
The Fazer is boring as hell. It's much faster but it makes it's power in a very liner way all though the rev range and has very little torque. The result is having to keep it around 10k-12k rpm which is screaming its tits off.
Around this rpm it is vibey and the reflection in the mirrors is just a blur.
Working on it is more fiddly with some things looking like a real after thought on yamahas part. For example, to remove the front sprocket cover to clear out crud you have you must remove the gear linkage that runs through a gap in the frame.
Undersea exhausts cost a fortune unlike the millions of cheap SV options. The standard can sounds crap.
Headlights are the annoying one light for dipped and both on for hi beam so people keep flashing you to tell you you have a bulb out.

Good things are they are pretty comfortable as stock.
The brakes and front forks are FAR superior to the SV.
It is really well balanced out of the box and handles well with none of that swing arm play the SV has.
I only use a bike to commute these days so the fazer is fine but if I ever go riding for fun again in the future I'll need to chop it in.