Wheel upgrade on a new bike
 

I am a clyde who is considering a new roadie. The lbs I deal with sells Cannondale, Giant, and GT road bikes. Any of them that I am interested in have like 20 spoke wheels. I asked about upgrading, and was basically told sure we can get better wheels but additionally not instead of. You would think that Cannondale for instance, being hand made in America could substitute a wheelset. So anyway is this typical, that with an upgrade you end up with a set of wheels to get rid of?

That's about the way it goes. The LBS isn't buying the parts, they're buying the complete bike. Therefore, the price is based off that figure. There's no "upgrade" price for a new wheelset because the LBS doesn't have an itemized breakdown of parts pricing for the bike.

You're best off just buying the new wheelset and either keeping the 20 spokers as backups/indoor trainer wheels, or just put 'em on Craigslist.

Not necessarily - a lot of time a lbs will give you a significant discount on the new wheelset because they can still sell that old wheelset. It may be additional but it should still be discounted.

Stout aftermarket wheels are pretty cheap from places like Nashbar, and you can get a killer set from Rivendell (www.rivbike.com) for not much more. They don't have to be super light, just strong, and almost anybody's "touring" or hybrid wheels will work fine.
I weigh ~240, and I've had trouble whenever I've tried to go below 36 spokes (probably because I ride dirt roads occasionally--I can use 32s if I'm careful of the surfaces). Rich Lesnik at Rivendell built me a rear wheel that's lasted more than 4000 miles without truing on my Atlantis. Having two wheelsets is sort of cool anyway, because you can mount different tire sizes and be ready for varying conditions in a few seconds. Here's one link; Rivendell has others: http://www.rivbike.com/webalog/wheels/18160.html

in my experience, the bike shop will let you upgrade for the difference in price, spec to upgrade.

They know what the "value" of an item is whether or not they get a breakdown from the manufacturer. (Or they know what they will be able to sell the OEM wheels for.)

It's been a few years (about four) since I bought a new bike and did this. Is this no longer common?

Avoid any/all interaction with www.Superspokes.com
I ordered a Ultegra - Velocity Fusion wheelset.......it has been over a month since my credit card was charged and still no wheels and no completion/ship date. Will not return phone calls........refuses to provide actual build status or completionship dates via email.
Learn to build your own or be extremely cautious in selecting a wheel builder.

Call a few other bike shops and see what they have in stock.

If you are not buying an expensive bike the wheel will not be that expensive anyway. Ride the bike around and if you like the frame then upgrade the wheels. Sell the old ones.

check craigslist/ebay and see if there is anything decent and used being sold locally. Use the money you save to upgrade the wheels. Phil Wood sells a nice rear hub with a extra thick shaft.