Well for part of that the Sahara issue needs to be fixed regardless, it's utterly ridiculous.
As for how to fix it, it would require a new mechanic. Not new to the series, but new to HoI4. I would propose something along the lines of the following (which will be incredibly underdeveloped in terms of balance, so judging it on that point is getting way ahead of ourselves here).
There should be 3 variables at play:
1. National Unity: this would remain largely unchanged, except to be more dynamic in terms of giving the player more ways to increase his NU and decrease an enemy's.
2. Resistance: this is the current partisan system, and would also remain largely unchanged. It broadly represents resistance to foreign occupation.
3. Dissent. This would represent domestic dissaproval and resistance to the regime. While this would be unlikely to take the form of armed resistance, it could affect factory output, party popularity, conscription rates, cause negative combat modifiers, affect build/repair speed, research speed, etc. It could even affect attrition as troops are more likely to desert an unpopular regime. This mechanic would be affected by conscription, economic mobilization, war length, strategic bombing (scaled based on the regime's response), and overall combat. Players could tighten propaganda laws, shoot down bombers, invest in consumer goods, take appropriate foci and other actions, and win important victories in order to lower dissent. Dissent would rise based on conscription and mobilization laws (which currently have no mechanic representing public order which they can affect), losses on the front (people don't like losing family and friends), unanswered bombing raids, political actions, national foci, and events, etc. Non-core provinces could also have built-in dissent increases so that simply annexing everything is no longer without repercussions from the populace.
This would add a missing variable to the current game, where foreign resistance and willingness to surrender are modeled, but not the plethora of other things that should be. There's simply no reaction from the population no matter what happens during the war short of surrender, when realistically drafting everyone who could hold a gun, for example, would be immensely unpopular and would cause a multitude of negative effects beyond training time and factory output due to lack of labor.
