I've found that I'm a little bit slower on my JM than on any of my other guitars. I think it's because of the relatively heavy string gauge I use - I use 11's but I've got 10's on most of my other guitars. The neck definitely isn't the big problem because I'm used to playing a lot of very different necks (Gibson type necks, short scale fenders, teles, rickenbackers, a 20" or 22" -ish acoustic and the Jag baritone too).
I've got this idea that the combination of 11's and the JM trem has this effect on me. Maybe because the trem on the JM doesn't feel like a stop tail, string-through or similar more "solid" bridge constructions that I've been playing for years before i got the JM
That said, if I want to shred on my JM I can still do it without too much of a problem. It just doesn't feel as comfortable as on, for instance, a tele. Still love my JM to death though, it's my main guitar and this probably won't change for years to come.