The way I see it, unless you understand what the suspension IS and what it DOES, taking it to someone to "set up" is a crap shoot.
What exactly does "set up" mean?
"service" no problem, he can do that: restore to factory spec
I would never take my bike to someone to "set up" the suspension. You're going to get a bike set up for the guy doing the setup.
Tell the guy you have problems with high speed harshness: he can deal with that.
Tell the guy you have too much/little spring: he can deal with that
Tell the guy the bike oscillates dropping into a corner: he can deal with that
Tell the guy to "set up" your suspension: WTF does that mean? Return to factory spec and set the sag? You SHOULD already have that.
I am all for using a suspension guy to help you solve your suspension issues, but YOU have to know what the issues are so you can articulate them to your guy.
RaceTech has a suspension textbook "The Motorcycle Suspension Bible" for sale on their website (or look for a free PDF online) that should be required reading BEFORE you do anything to a bikes suspension... if for nothing else read it to get the nomenclature so you can explain to your suspension guy how you screwed up your bike
To pick on
@Relax in particular: When you say "John sets up the suspension on the stiff side by default" do you mean too much spring or too hard damping?... and do you know the difference?
IF
@Relax set his sag himself and was comfortable doing it, he could easily take a 14mm wrench and take some spring out of it to test if it was spring or damping
Other than some basics, suspension is mostly subjective. what I want is probably different from what you want, so really, you're on your own, so if you want good suspension you have to figure out what good suspension is... and good suspension is like good sex, you don't know what it is till you've had some.
... and from experience: it's cheaper and easier to take off lap time with suspension than motor... and it all starts at setting the sag.