Ok so my trip to the LBS was scary and I'm glad I made it out alive. I spent two days browsing bikes locally, went to the LBS and ended up looking at a specialized hardrock sport 29er. Two days talking and they quoted me 520 bucks for the bike, I was happy. I ran to walmart for a bike rack as that is what they suggested while they fine tuned parts. I had hydraulic disk brakes, air forks with lockout, double wall rims, I felt really good about my purchase. Then I got back, and was told 640. I showed them the paper they had written me but was told the bike was not what they thought it was and there was a mistake, they offered to go down to 630. I felt that was a bit shady so I left, on my way out to the parking lot, one of the guys inside said he would sell it to me at a later date for 520, I just had to wait for a day when he was working alone. All felt really shady so I decided it was time to go. Went to the local scheels and picked up a trek 3500 disc. The next day they called me in and put me on a marlin 5, it had gone on sale and was actually 30 bucks cheaper than the 3500D, so I am now the owner of a Trek marlin 5. My only issue is, I don't know the sizing very well. When I stand over the bike in sock feet, there is light contact with the top tube, and the seat tube has to be bottomed out to fit me well. It says "actual 16.5/vertiual 17.5" on the down tube. The next size down a 15.5act/16.5vit uses 27.5" tires instead of the 29" on this bike. I'm 5'6 and have a roughly 30-31" inseam. Did I get sized right at 17.5 or should I step down to the 16.5 actual?

Bottomed out seat tube is generally a bad sign. I'm 6'0" and found a 19.5" Trek to be about right for me, so the 17.5" is probably at your upper end.

When you say the seat tube is bottomed out, if you put your heel on the pedal your leg should be almost completely straight? With a properly fitted bike, you will not be able to put your feet flat on the ground while seated, at best you'll be able to put a toe down.

As for sizing, can you test ride both? If so get the that feels most comfortable while riding. Mountain bike sizing is generally more flexible than road bike sizing, so its likely that you can get a decent fit on 15.5, 16.5 or 17.5. The real question is your personal preference for wheel size, which is a personal feel issue.

The Marlin is a good bike, enjoy whatever size you get!

yeah seat tube all the way down, I can just get the ball of my foot on the peddle. I think the next size down with 27.5" wheels would be a better fit. Everything seems just a bit "long" to me.

Yeah, you might even want to test the 15.5 size.

There is no 16.5, so I went with a 15.5, they had a sale for 450 on the marlin 5, the six is nice, with the lockout forks and hydraulic brakes, but it was 610. I'm fairly sure I can live with mechanical disks and use the 160 bucks I saved for better forks, am I correct?