Zermatt/St Moritz in September ? I was there in April and we had snow in the towns, went up Gronergrat to 3200m and the temperature dropped to -24 degrees, but it felt hot in the sun and took my breath away... Killed my Fuji camera up there, be very careful. Also been up the Swiss passes in July, snow at the side of the road was quite unexpected ;-)

The Glacier Express is nice, but we have been back since in a car and enjoyed the freedom of being able to stop anywhere. Sit on the right if departing from Zermatt for the best views, but you will have sun reflections on that side.