Here's the thing:
At the introduction of the iPhone 6, Phil Schiller stood up and said that M8 could tell the difference between walking/running and cycling. As of iOS 8.1 it cannot. So in essence they are breaking their promise on that. Whatever, that kind of automated tracking was likely never going to work anyway without using GPS IMHO. If you'll ever tried the app "Human" it attempts to do this, and the results are mixed honestly, for example, when I went on a downhill section that was fast with no pedaling, it would say I got in my car do it!
Now, this shouldn't be a problem for people like me who use HealthKit enabled cycling apps such as Cyclemeter or Strava while cycling. However, in this use case the Pedometer simply doesn't work. Every time I ride my bike, the pedometer continues to count my pedalling motion as steps, and my hill climbing as "floors climbed", so I see big spikes and bad data.
Now if HealthKit could figure out that it shouldn't count the steps that are taken while I'm on my bike that would be great, especially as I'm using an app that tells it when I'm on my bike. In fact, Cyclemeter has a built in pedometer that seems to do this, and it's values for steps taken always seem quite realistic (it uses m7/m8 to do this) compared to Health's values on days when I ride my bike, presumably as it's smart enough to know that when I'm riding my bike, I'm not walking at the same time.
As of now, iPhone 6's / HealthKit's pedometer is broken for cyclists IMHO.