I love WiF; it's a fantastic mod. I can only imagine the hours Fernando and 49h, and others of course, put into it. Well done guys and don't give up on HoI2 please!
Anyways here are some of my open-ended suggestions.
Cohesion: Divisions which are grouped together under the same commander receive a cohesion combat bonus due to gaining familiarity with nearby units.
Example: 1. Panzer Division and 2. Motorized Division are grouped into the same unit 'Panzergruppe Hoth' and conduct several battles. Along with experience, these units gain a certain bonus for cohesion. If they were then split off into individual division-sized forces, they would lose this bonus (but of course retain their experience). Cohesion would also be reduced by reinforcement.
Upgradeable vehicles: Tanks can have new guns fitted to existing chassis. Factories produce abstract 'weaponry', which is used to upgrade existing divisions without converting to a new model.
Example: Panzer IV chassis with new weaponry gives more hard attack (ie converting to long barreled 50mm). Add even more weaponry to upgrade toughness (schurtzen to protect tank tracks).
Obsolete Equipment: As new models become available and divisions are upgraded to modern equipment, old equipment is maintained in supply depots. This equipment can be used to raise new formations.
Example 1: 12. Infantry Division is upgraded from '36 to '39. The old '36 equipment goes into storage, for minimal supply upkeep cost. Garrison divisions can be cheaply raised using cast-off equipment.
Example 2: Heinkel 111s are superceded by Ju-88s. The Heinkels could be used to create specialized air units. Add new weapons (torpedoes, cluster bombs, radar) and you have low level convoy raiders.
Example 3: Panzer 1 chassis have new weaponry added and become self propelled guns.
Specialized factories: Individual factories can be set up to produce specific armaments. They could gain proficiency for doing things for a very long time at a stretch. It seems silly to go from producing tanks with your entire industrial might, then switching overnight and making battleships with no penalty. (Gearing bonus could relate to individual models only. Overall bonus to making armoured vehicles, gearing bonus to producing Matilda tanks, for example). This could be worked in with peacetime penalties to effective ic, etc.
Linked command/formations: Create a semi-permanent link between units
ala HoI3. HQs could become attached to 2 motorized corps and an armoured group. This would work well with cohesion (see above). It's great for roleplaying too. Then, if units get too far away from their commanders, they lose their bonuses. Another reason to make a flexible command tree is the ability to earn experience on multiple levels. Mj General, Lt. General, General and FM are all either directly or indirectly affecting the outcome of a battle, so they should all gain some exp, and in different areas.
More stats for leaders: Leaders should be slightly more complex. Tactical versus strategic skill for instance. This would make the decision to promote much more interesting, as small unit commanders would make very bad field marshals. Some leaders could have infantry tactics, armour tactics, etc. or perhaps be really bad at using armour, but exceptional at infantry assaults. (Offensive Doctrine trait is too vague)
Peacetime exercises: The ability to conduct maneuvers. Get a certain number of divisions together and conduct a 'maneuvers' mission. Units and leaders gain exp, but it costs a lot of supplies/oil and makes you lose org. Can adversely affect diplomacy too, especially if there is no 'fog of war' on the territory you are conducting the maneuver in.
