OK. I played another game of my  "tiered setup" last night and wanted to share the process. I think it reduces the overall difficulty somewhat, but I need to do additional testing.

Tiered Setup:

1. Set aside the Escape Pod, Data Device, Navigation Module, and Power Cell cards.
2. Divide the Threats into three even piles of seven cards:
   1. 2x Distortion, 2x Fractal, 2x Residual, and 1x Void (the Easy pile);
   2. 2x Void, 3x Silhouette, 2x Spectral (the Medium pile);
   3. 1x Spectral, 2x Corrupted, 2x Aberrant, 1x Chimera, 1x Amalgam (the Hard pile)
3. Shuffle the remaining Weapon, Healing, Gear, and Situation cards together. Then randomly distribute them among the Easy, Medium, and Hard piles.
4. Shuffle the Escape Pod and one random Essential Gear card into the Hard pile. Shuffle another random Essential Gear card into the Medium pile, and the third into the Easy pile.
5. Put the Hard pile into the play area, place the Medium pile on top of it, then place the Easy pile of top of that.
6. Play as normal.

This setup means the Escape Pod is in the bottom third of the deck, and one piece of Essential Gear is in each third of the deck. Threats increase in difficulty as you progress, but, just like in the normal setup, there is no guarantee the Weapon and Healing cards also increase in value. It also means there likely will be Residuals in the discard pile when you encounter a Silhouette (putting them on the bottom of the deck). Distortions, while easier to deal with as you encounter them early in the game, have a huge effect if you sneak past them, since shuffling the deck completely destroys the increasing nature of the Threats.