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You get an extra gear. It kind of depends on what year models you are talking about as a lot of people who bought 07's had problems with the 6 speed. Do a little research around here. I have a 5 speed and it's fine for me.
what kind of riding you anticipate doing? Have not tried a 6 speed but the 5-speed is just fine for the kind of riding I do (DD to commute to/from work, ocassional weekend jaunts, etc.)
The 6th gear on the stock 6-speed tranny is the same gear ratio as the 5th gear on the stock 5-speed tranny. They tightened the ratio between gears so the step up wasn't as big, thus keeping you in the fat of the power zone when shifting, rather than on the edges of it.
I use my 6th gear often. I was always stomping my 5 speed trying to get another gear out of it, now it's there. If you can get a good deal on an 88b 06 go for it. If not look around lots of good deals out there on 07 and up.
The 6-speed Cruise Drive transmission, which was introduced on the Dyna family in 2006, features gear ratios optimized to match the torque curve of the new Twin Cam 96/96B engines. The addition of a higher-ratio sixth gear reduces top-gear rpm by 11 percent, compared to the previous 5-speed Big Twin transmission. At 75 mph, engine speed is reduced by 368 rpm, from 3227 rpm to 2859 rpm. Second through fourth gears have helical-cut teeth for quieter operation, and load carrying capacity has been increased significantly.