I don't like the infantry- base troops seem like upgrade reliant Volks, engineers seem to be Sturms. It makes sense to just make engineering part of an upgrade path for the core infantry somehow, building on the flexibility theme.
I like this idea, making a single modular infantry unit kind of like Panzer Elite but various specialized paths depending on unlocks and upgrades. The idea I got was this:
-Like Panzer Elite, there is ONE actual stock unit, but it comes with 2-3 free upgrade paths depending on what is available in design and commander unlock. You got builder path and combat path; further paths can be obtained via weapon racks (ie LMGs make them good long range combat) or doctrines (a commander allows SMG upgrade alongside builder or combat path).
-A more versatile set of basic capabilities, for example all variants can repair stuff, but only the ones you have upgraded to dedicated builders will be best at them, and certain doctrinal unlocks involving repairing. building stuff would only benefit your builders
-Upgrade paths determine a large amount of what this unit can do: upgrade the squad to combat and they can't repair as fast nor can they build emplacements besides basic sandbags or wires etc. The upgrade paths can be free so as not to have a tremendous economy burden; instead of starving yourself of resources trying to get builders, you are pressed for time.
-This sense of versatility might actually be a bit historically fitting, given that a lot of Luftwaffe ground troops were just re-purposed air and ground crews with little combat training.
-In contrast, call-in units like Fallschirmjaegers, whilst still having rather versatile in combat abilities, are the best fighting squads you have.
I also think the officer should be the cornerstone of the army, and that "specializations" should just be fuel based upgrades like with the Brits.
More on the officer: it would be neat if he could give off different kinds of auras depending on his level/upgrade/doctrine, like a "Zeal" aura where units fight harder but die faster, or a "construction" aura where buildings and repairs and maybe capturing are done faster. Slap him in a 250 Halftrack and you have a solid commander that can zip around buffing different parts of the army at ease.
I would make the officer less about active abilities and more about passive ones, and auras.
I like this idea as well, it requires less micro on a single "hero" unit's special abilities, but still gives him a versatile support role for the entire army all throughout a match, rather than the CoH equivalent to a Space Marine Force Commander. And those special abilities can also just be divvied up and relegated to doctrinal unlocks, ie Entrenchment Doctrine allows him to set up retreat point while an assault-based commander lets him use Concentrated Fire.
EDIT: an additional note regarding my Hetzer/ Marder comments:
In terms of historicity, the Marder III was more of a stopgap/ economic complement to more capable tank destroyers, so it could fill the same doctrinal role as the M10 does for M36- the Hetzer can camouflage, can upgrade to top gunner, and moves faster; the Marder as doctrinal call-in is available earlier, cost less, but less maneuverable/fires slower and more fragile.
If you REALLY want it to be an either/or choice, you can always apply the unit swap doctrinal theme I mentioned earlier, and have the Marder replacing the Hetzer if you choose the appropriate commander; you got the unit swapping thing going, yet without the inflexibility of the other abilities to consider.