When the pavement gets too bumpy the Canal Corporation scares up some money and repaves it. This alternates as sections get bumpy. Right now, one section has gotten bumpy enough that you need to exercise caution: between Kendrick Road and East Henrietta Road. I would still recommend using the canal trail, but watch your speed and avoid the bumps if you can.
The road alternative over this part of the trail, NY Bike 5, is a horrible route. It uses Elmwood Avenue and Monroe Avenue, both of which have no bike lane and four lanes of medium-to-heavy traffic. Drivers on western Elmwood, around Strong Hospital, seem to always be impatient and intolerant of bikes. So stay on the trail, but stay on your toes.