Either way is totally fine. The wind comes from the west but is usually pretty minimal going down the parkway. Terrain wise I feel its a little bit easier to go from Jasper to Banff, and you get to go down the sweet U bend around the Icefields That one is a riot! Jasper to Banff seems to be the more popular route as well when on bike.

However if you are going to ride from Edmonton to Jasper, I will say this (I'm from Hinton). The wind from the park gate to the Jasper townsite can be awful and unridable at times. I have rode that part of the Highway 16 many times and had to turn around a couple times even unloaded. 50 to 100 km/h wind gusts are pretty common and so is getting blown off your bike