I think you're making it convoluted by having two 'types' of upgrades that mostly change things in the same way. A way to simplify might be to separate them in such a way:
- Ideologies (probably need a different name, though) affect what units and buildings are available to you (changes your available techtree) or alter your economy (resource gathering, using, trading). These are high-level upgrades that you might only research a couple of in a game. They are more akin to choosing your race in wc3 melee.
- Doctrines alter/upgrade/augment the units that are already made available to you by your ideologies. These are more micro-oriented upgrades that can be used to counter/react to opponents' strategies or push a play style of your choice. They are more akin to upgrading damage/armor/spellcaster mastery in wc3 melee. Most doctrines are ideologically-agnostic (available to all ideologies) but some require a specific ideology to use and will become unresearched if that ideology is removed.
As an example: the Fascist ideology opens up the German techtree and the Communist ideology opens the Soviet techtree; if you have an 'Americans'/'Great Britain' analogue I'd perhaps call it Nationalism (rather than "Capitalism", but that's just me). These are mutually-exclusive but each have roughly analogous units available with some minor stat differences. Think Age of Empires 2. There is also a "Strike First" ideology that adds scouting units to your techtree, and allows researching of 2 doctrines that increase the sight range and movement speed of your units. There is a "Defensive Posturing" ideology that adds attacking towers to your techtree and allows researching of 2 doctrines that increase the armor and sight range of your structures. While the German/Soviet/GB trees have some basic naval and air units, there are also "Naval Specialization" and "Air Specialization" ideologies that drastically increase the types of those units a player can build.
Excepting the ones that are tied to a particular ideology, the doctrines available to be researched by each player have a different effect depending on what ideologies are active for that player. "Blitzkreig" increases the move speed and damage of Fascist Tanks, allows Communist tanks to garrison troops, and increases the production speed of Nationalist tanks. "Anti-Air Encampments" allows "Strike First" ideologies to quickly build fragile AA towers with their scouting units, and for "Defensive Posturing" enables a secondary attack on their towers that's highly effective vs. air units. Some will be the same for all ideologies: "Armor Piercing Rounds" changes the attack type of infantry units to better combat vehicles.
