Before development gets too far, I think now's the perfect time to avoid the generic arpg difficulty system of cranking up the health and damage of enemies to make things "harder". It simply does not work in Martyr because Martyr isn't a generic arpg. The cover system, charge based utility items, suppression mechanics and direct combat all only work properly when tuned to a specific amount of enemy health and damage.
How to make things more difficult then, since variable difficulty is certainly a desireable feature to have?
My proposal is that, instead of increasing health and damage of enemies and thus breaking the various unique features of the game:
Difficulty increases the frequency of champion and elite enemies. For example, an "easy" mission might have no big dreadnought/Tank sized champions at all, while Space Marine/Ogryn style enemies would only show up in singles every couple of rooms. On a "normal" difficulty mission, Space Marines would be in most rooms, somtimes in multiples, and the mission would usually have 1 big dreadnought sized target. "Hard" missions would have elites in every room and multiple champions.
Additionally, what kind of abilities and types of enemies show up would also be tied to difficulty. Ground targetted abilities that require the player to move, for example, could be entirely or nearly entirely absent on "easy", while they'd be fairly frequent on "hard" (requiring more player skill and input).
Third, harder difficulties could have rooms with enemy mixes that don't exist on easier ones - such as strong ranged elites combined with swarms or other synergistic combinations of enemies.
Those 3 things combined, as well as dropping the generic health and damage percentage boosts, would make for difficulty levels that still present variable challenge (and reward) to the player, without making limited weapon charges, suppression and cover health impossible to balance for all difficulties.
Instead of % boosts to stats, make harder mission enemies more formidable through type combination, AI and ability use, because it's impossible to properly balance unusual mechanics with variable enemy damage.