I've had two "professional fittings" and I would characterize them differently. One was for a bike (which didn't fit me, btw) I already had. It was about 60-90 mins long--but was pretty basic. For the fit and components I dropped about 230$ (I think the fit itself was 50-75$). Basically this type of fit is used by dealers to either match you to an off-the-shelf bike they have, or if you already have a bike they will make recommendations (the stuff I bought, new saddle and insoles I was going to buy anyway--so I didn't feel like he was a salesman). This type of fit definitely makes them money for either a bike purchase or components, because 50-75$ for 60-90 minutes of a fit guy's time is practically them giving it away. But, like I said the guy wasn't a salesman at all--and he mentioned this as well. Good fit guys are pretty professional about it.
The second fit I had was with a Serotta guy who has been selling Serotta's -forever- and is one of Serotta's few "advanced fit technicians". I brought my bike, shoes and some water. The Serotta fit, or at least this guy's version, is very "holistic" (imprecise term, but it's all I got right now). It took about 2hrs, possibly longer. For a good portion of that time I was pedaling on the Serotta size cycle. They also do an interview and ask a lot of questions. They have various devices and lay you out on a massage table and stretch you various ways. He also had me stand in various positions, balance in certain ways, go from seated to standing in certain ways--lots of different stuff. He also gave me -lots- of tips about my pedal stroke, adjusted my cleats and pedals at least once. Showed me how to correct some of my positioning, and told me various techniques to improve my balance. Overall it was a great experience. I think the cost was $175.
As far as design, it is basically up to you--but, they will try to steer you from stuff they know (from experience) you might like aesthetically, but won't like when you ride. The first draft of my bike probably had a bit more headtube and slope than I would like. I searched tons of Serotta pics from the serotta.com forum and bikefanclub.com gallery and emailed him examples I like. They are pretty firm about certain stuff. He showed me a Fierte (and even said a Fierte would sorta fit me if I didn't want custom) and I said "that's a lot of headtube" and he kinda laughed "Yup, you're gonna have some headtube" (but I think this is also going to be changed.)
My first plan was to get a Colorado 3 (aka CIII) with the pimped out Lemond-like paintjob below--exact colors and style.
I decided instead on the Titanium Concours, which is Serotta's mid-level Ti frame (Fierte [no custom geo] $1800, Concours $2500, Legend $3400). The main reason I chose Ti was not for it's "pimp" value or even weight considerations, I chose it mainly because it is so low maintenance without paint. And I am getting mine unpainted with only two decals, so worse comes to worse I just order new decals--no paint to worry about, no rust, no corrosion, can ride in snow, rain, salt, etc. I also chose Ti because I won't be afraid to push myself on the bike--if I crash I can just buff out any scratch with scotchbrite or steel wool. This bike is WAY too pimp for me (I'm not into flashy stuff, or wild looking/etc stuff). I am getting it with only downtube decal and no seat tube or chainstay decals. Whatever wheels I get will probably have the graphics removed (ksyrium sl's would look sweet without decals). Also, I'm not the type to spend this kind of money on a bike, but have decided to for two reasons 1) I will probably be off to grad school or law school soon. I will have almost zero income during that 2-3 years, and will be unable to buy another bike during that period. and 2) I want to close the "bike box"--handle this thing and be done. Once I get this bike it will be COMPLETE, and I will focus exclusively on my riding (and focus my posting in the 'Training and Nutrition' forum). I'm not the type to be tinkering or upgrading or swapping stuff out. I will be done with looking at bikes after I buy this one (and then buy a Parlee if/after grad school

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I also considered Seven and Moots. The Seven dealer in town are punks, and Serotta has more experience and a much more open owner community, and just community in general. The Moots was 300$ less but wasn't custom and you can't specify tube types. With the Serotta you can select -everything-, geometry, tubing types, paintjob, badges and/or decals, etc, etc. Also the finish on the Moots apparently scratches and Moots offers a refinishing service for this. The Serotta is just polished, no finish. My second choice would have definitely been the Moots though, I was very close to getting a Moots when I spoke with the Serotta dealer I eventually went with.
As far as eliminating flex/whip from Ti, lots of mfg can build with oversize tubes to eliminate this--I will probably opt for this. If you look at first generation or second generation aluminum frames, they weren't always built oversized like they are now. A lot of Ti builders are using larger tubes as well. Serotta, in particular, is good at building clyde-friendly Ti frames.
okay, long post. It will look like the one below, except only decal on downtube. Very plain jane. Titanium like a mack truck, not a piece of jewelry.
I'm also a firm believer in spending your money on the frame. Like someone else said (paraphrase) "Would you rather have a fully-loaded Yugo, or a base-trim Mercedes?"