I don't think it really matters much. In August, we did the bus ride up and the train down. It was rainy and foggy in Skagway (but beautiful up on top of the mountain) so we still experienced some fog on the way down on the train.
For us, I think taking the train down worked fine. On the bus ride up, there was a lot of getting on and off the bus for pictures, etc. Then in Carcross, we were walking around seeing the puppies, looking in stores, etc. So the train ride down was relaxing after that (although I still spent a lot off time standing at the back of the train, LOL). When we arrived into town, we were rested and ready to do a bit more shopping before heading back to the ship.
But I'm not convinced that it would have been much different if we took the train up and bus back (since the last part heading into town on the bus would have been pretty much the same).