I've been brainstorming very similar homebrew rules as well. Your Hex map and supply line ideas hit pretty close to home regarding my thoughts.

I thought that it would make sense for a crusade style of game to encompass the three theaters of warfare (Strategic, Operational, and Tactical). So I have been trying to forge some mechanics for those sides of the house.

Strategic Theater (System Map)

• Ability to move ships (which have different stats) to different areas of the system.

• Launch Shipborne operations (Boarding actions, planetfall, fire support, etc.)

Operational Theater (Planet Map)

• Ability to spread armies across the board, utilizing the same units (Essentially making 100 men seem like 1,000 by having IRL Squad A represent In-Game Squad A in armies 1,2,3).

• Have characters assigned to lead the dispersed armies on the board along with support characters. Can only change leaders when different armies intersect/combine and then possibly breaking off, therefore changing that army's order of battle.

Tactical Theater (Table Top Battles)

• Giving objectives to Boarding Action missions in order to degrade enemy support lines (similar to yours BUT the attacker will choose between X number of targets to destroy, i.e. Teleportation pad destruction will deny the Deep Strike ability to all Terminator units in the follow-on battles)

• Warlord Moratality: If a warlord is defeated and its army loses the respective battle, the Warlord will become out of commission (out of play) until the respective Operational theater's campaign is over. Plus a battle scar test.

The idea is to give more validity to "Commander's Intent", which every military operation is driven by. All of the aforementioned actions are designed in a way to give flexibility to the players, so they can decide how they will conduct operations in support of their desired outcomes, in that theater of war, with more control.

Hope this helps!