This is something I've thought about off and on and tried to implement various ideas in mod tools. I could never get things to function how I'd wanted due to the restrictions of mod tools/my own time and knowledge of modding this game.
I honestly believe that while there are obviously some broken commanders on either side of the viability spectrum, I don't think that individual designs of commanders are the root of the problem.
I think the most distilled version of what might function for CoH2, not necessarily a hypothetical CoH3, would be the return to how vCoH utilized CPs.
You didn't choose a doctrine that automatically unlocked abilities as you acquired CPs. You acquired CPs, and then you used them to progressively unlock abilities from one of the three doctrines.
For CoH2, since commanders don't have branching/multiple paths of unlocks, it would actually be feasible if ALL THREE commanders in the loadout could be unlocked in one game. You would have three pathways to spend CPs on. You could have your Soviet Shock Army where you spend 2 CPs to unlock Shocks, but then you could have the community commander with tank traps that you could spend 2 other CPs on. And then hell, you could have Guard Motor to unlock Guards.
6 CPs in you could have Shocks, Guards, and Tank traps, but at the same time you'd be a long way off from any ML-20s, T34/85s, etc. This setup would allow for players to spread their CPs out for a wide array of useful passives, like say, Riflemen mines, RE flamethrowers, and M1919 unlocks. But the endgame abilities and call-ins would be likewise delayed. That M10 might just come too late.
Do you put everything into one commander to get out that Elefant? Do you get your Panzerfusiliers out then switch gears to try and get that Sturmtiger or Command Panther unlocked? Spreading CPs too thin could be crippling.
I always thought this would've been far more dynamic and interesting for CoH2. This is how I felt in 2013.
My OTHER notion about commander loadouts would be that all commanders could be categorized in a mutually exclusive way. For example's sake, all commanders could be categorized as "Offensive", "Defensive" or "Support". All loadouts would consist of one "Offensive" commander, one "Defensive" and one "Support".
All in all, I kinda miss triple NKVD commander loadout scare tactics. Kappa.