The helix will only be out if you have to run full-length Powder River unit trains. If, like me, you make a conscious decision to run short trains with LOTS of motive power you can put a helix in one corner and have it as small as 460mm radius (and 3.5% grade.) Think logging or precious metal mining on either the upper or lower level, with more conventional railroading on the opposite level. Helix can rise one inch in 90 degrees of turn, as many turns as necessary.
A twice-around 2.5% continuous grade will give you a railhead to railhead distance of about two feet (levels at 36 inches and 60 inches.) 2.5% is steep, but, again, lots of motive power. The prototype assigns helpers as necessary.
No one has mentioned a train elevator. It can be as long as your longest tangent, have a footprint six inches wide (if built with steel stud material) and can be as tall as you’d like it. A little inventiveness can put safety tracks into place when the car is at the other level. (John Armstrong preferred solid gates.)
As a last resort, you might consider building two levels without connecting track and connecting them with cassettes operated like car floats. Once again, your train can only be as long as the cassette it goes into.
I have, or have had, all four. The easiest is the long, sustained grade. The cassette transfer is the biggest pain in the rudder post. The elevator will require greater precision and more maintenance. With a tall helix, there’s a certain amount of, “Where did the train go,” as it spirals 'round and 'round. All of them will work. None will be perfect.
If you absolutely, positively have to have full-length Pullmans, double stacks, humonguboxes and a Schnabel car, none of the above will work. You need to keep those on a single level.
Chuck (Modeling Central Japan in September, 1964 - short cars, steep grades)