It kind of depends on what your GPA and projected score are to determine if the September MCAT is too late. If you have a lower GPA and/or lower projected MCAT score than it's better to apply in the summer and since you won't get your scores until october and then will still have some secondaries and whatnot you may be looking at November to December until you are complete and that's when competition is very high.
As far as the person asking about January MCAT scores, yes some schools accept them but I would not recommend doing this because you won't be complete until February or March and most schools will have their interview dates filled up or will just be interviewing for waitlist spots. However if you are put on waitlists and you want to improve your application for the following year you can take the January MCAT and send the update to the schools which may help you get off the waitlist.