I have a similar issue. Some of it is lack of stretching perhaps, because running or any kind of workout as I have read reduces your flexibility.
But beyond that, you have more muscle in the way now, and you are going to lose some of your overall agility and so on just from that alone. I have a harder time washing my back etc etc
On a larger more obvious scale, look at a pro bodybuilder, do you think those guys can move as around as well as you can and such? Some of them can do the splits, but with those biceps they can lift thier forearm up about half way