Breakfast queue wise, we usually go for an early slot at both hotels to make sure we don't end up in the huge queues!.
We had to stand in the Santa Fe huge queue last summer once (breakfast in the park for the other days) but the slot was a late one.
We've had to queue a fair while at the Cheyenne too, but I don't think their queue was outside!.
Both hotels are the same to me, except for the themes. But the creaking floors in the Cheyenne creep me out :| I know its all part of the theming but still..
But then again I don't like the Santa Fe if we don't have a close block to reception.
So I guess it just depends if you're a scaredy like me :').
Bus wise, Cheyenne is better (easier to get a seat), but the Santa Fe have a queueing system now too which makes it a bit more manageable.
I stay at one, one trip and the other the next trip so I can't really help say which is better. Although, from a scenery and/or photography point of view i'd say Cheyenne, just because of this photo that I took -
http://elstoleno.deviantart.com/gallery/26246761?offset=48#/d2wibox (too big to insert as a image nicely I think)