I first put some of this in way back when we were discussing wish lists for HOI2:
Ships
Combat: True naval combat, rather than kludged land combat, needs to be realized. Look at Grigsby's War In the Pacific for some ideas. Keeping CAGs attached to CVs is still a good idea, as HOI1's floating airfields for B-29s was a farce. Proper CVEs, which were used as ASW escorts in the Altlantic and invasion fleet protectors and shore bombarders in the Pacific, need to be included. Not sure if CVLs are absolutely required.
Upgrades: This idea that ships cannot be upgraded is absolutely ahistorical. Ships had continuous upgrades in AA, radars, gunnery control and even range (coal to oil conversion). Of course, to be upgraded, a ship must remain in a large-enough port (say Size 10 port for BBs and CVs, lower for others).
Production
Factories: The production of ships, aircraft, armored vehicles, trucks (for motorized brigades and artillery, perhaps others) and small arms (to equip divisions) needs to be modeled. Say the U.S. has a factory that takes a 2 IC/day input and puts out 10 ea. P-26 Peashooters a month in 1936. That one factory could be upgraded over time by say a maximum of 10% a month (with proper IC and $ investment). Then the model could be changed to P-35 later on when the tech is available (that would create say a one-month retooling downtime and the rate would be say 20% lower once it got going again due to the more complicated aircraft). Starting an entirely new factory would require a sizable investment, and total factory output might be limited based on total ICs (industrial tech and "Rosy the Riveter" tech would increase allowable number of factories as a function of IC). With each incremental change to a war-footing, the conversion of a number of existing civilian factories would be allowed for say a 50% discounted investment (representing Ford switching from cars to tanks and B-24s, for instance).
For ships, you'd create and upgrade shipyards that could build ships up to a certain size on a maximum number of slips. There would be no ability to instantly shift production from ships to tanks to aircraft as is the case in HOI2. You could always put factories/shipyards in sleep mode (for some continuing cost) or shut them down entirely if your priorities changed.
Force Pools: The equipment built by your factories would then go into the force pool which would be drawn by new divisions and air units and be used to upgrade existing divisions and air units (at the brigade level, as they say brigades are now possible). Leg infantry brigades could be converted to motorized with the addition of trucks. Your exchanged equipment would be put into the force pool, where it could be used again for line units in emergency or converted to scrap metal and rare materials.
Some of these ideas come from Grigsby's War In Russia and WItP, which are fine games but lacking the all-encompassing strategic nature of the HOI series.