Trek and no Deep Dish Wheels

For those spending that type of cash, they are likely willing and able to select and buy their own wheelset of choice.  Why raise the total cost of the bike for some when they have no interest in the wheels provided?

Take a look at Project One. It's their custom program. They have loads of options in there. You can put any Shimano or SRAM drivetrain on. They used to have Campagnolo too, but looks like they dropped that off. Lots of wheel options in there too from a very basic box set up to Aeolus 9. What you see listed in the completed bikes are some basic stock options with considerations like JohnnyKay mentioned. $5,000 isn't quite their upper level. That only buys their top level frame. And that's the case with other brands as well. Not all, but Trek is not alone in this.

Like Brigby said, Project One custom builds have deep dish options.  The choices are Aura 5 (50mm clinchers with aluminum brake track), and the high end Aeolus D3 full carbon wheels (clincher and tubular) that come in sizes 35, 50, 70, and 90 mm.

Jr. has a Madone 5.9 for DL racing.  The Bontrager Race Lite wheelset is comes with is actually a pretty solid set of wheels and we've been happy with them. (if a 17 year old boy can't break the hell out of something then I feel confident calling it solid)  Since we already own a few sets of deep  wheels I'm glad it didn't come with upgraded wheels and push the price past the $5,000 mark where it already is.

I've bought more then my share of higher end bikes the last few years as my kids have continued to grow.......one of the best things I did was find a few sets of really nice race wheels at a good price that work across the board.  Shop, shop, shop and you can find barely used Zipp 404 firecrest wheels for 1,000 - 1200 bucks barely used.  The best part of buying equipment for bikes is that the market is flooded with barely used high end equipment that you can buy for a fraction of retail.

The real problem with the high end Trek bikes is the stupid bontrager integrated brakes.  If you buy one.....just switch them out for Ultegra or Dura Ace brakes and throw the bontrager brakes in the trash where they belong.