Was there in September of 2005, right after Labor Day. Steam was done for the season and our 8-car train was pulled by a single F40PH. Got over the road okay, but it was pretty obvious the F40 was down on her knees on a couple of the grades. Our train had one of the ex-CN generator cars right behind the engine for HEP, so the F40 had all 3,000 HP available for traction.
Good part was the weather that time of year is outstanding: not too hot, not too cold.
Spend the extra $$ for the first-class obs car, especially if you have non-railfan family members along for the ride. Well worth it and you can shoot off the rear platform all you want.
If you do the overnight at the south rim (also recommended), the resort "that is not the El Tovar" (they're all owned by Xenterra, as the railroad is now) has cabins along the south leg and tail of the GCRY wye. I got to shoot the AOE arriving and turning on the wye from my cabin window.
The El Tovar, a former Harvey House hotel, is also a must-see: It's a little pricey to stay there, but a meal in the dining room (reservations required)and/or a cocktail in the lounge will give you a taste of the place (no pun intended) without breaking your budget.