Shortcuts in the main facility
Within the main facility there are various vertical shortcuts you can take, for speed or stealth or just a bit of variety.
Hole descent to the Hunter chamber
At the back of the first room you enter, there's a well-hidden hole in the floor that lets you drop down outside the Hunter chamber. It's a sneaky alternative to using the ramp, and gives you a nice way of taking a few Jackals by surprise, or bypassing them entirely.
Off the edge outside the Hunter chamber
By the supplies outside the Hunter chamber, there are several ways of dropping down. If you've got an overshield, you can actually drop down all the way to the bottom floor, to reach the Silent Cartographer. You'll land near another overshield, which may come in handy. You can also get down with no damage to health (or overshield if you've got one) by making a few lesser jumps. Also, if you've already been down and you bypassed enemies on the way up, you could now jump a few feet down onto a ledge on the left, and potentially surprise some enemies below.
Big drop after the Hunter chamber
Just past the Hunters, a walkway starts to lead you down. But after that first short slope, look down. There's a drop that looks much too big to survive. But you can make it without any health loss if you land on a small bit of sloping surface at the bottom. Slope helps break your fall; it's less of a shock to the system. Once down, the Elites guarding the Silent Cartographer are just a short way away, around to the right down a ramp. When you spot them from the bottom of the ramp, you could maybe send in a few plasma grenades; it's pretty easy to tag at least one of them.