Being a bit out of shape while still being in your prime is entirely possible. Look at many young athletes in the off-season, especially football players, they often get a little soft, but can easily whip it together when the season comes back around.

Remember, Kakashi has had to babysit a pack of Genins for a LONG time, which means a lack of difficult missions and time to dedicate to Jounin-level training and activities.

Imho, Kakashi is in his prime, but has been neglecting his potential for a while. With the action heating up, he will probably be increasing his skill set accordingly.