Air Power and Logistics
Air power was the dominant force in the historical campaign and should be in the game. Logistics are also important and affect airpower and every other kind of force.
However, there are a number of flaws and known bugs with the use of aircraft in the game. Hence, any strategy designed to create overwhelming air superiority and win the game by using airpower winds up encountering serious efficiency problems. This is a logical paradox, and would cause me to shelve the game if these things are not fixed.
Strafing
Strafing by most any kind of aircraft at most any kind of target, particularly ground targets, results in some errors. There is the notorious "Akagi" error. Strafing of barges by cannon-armed fighter-bombers or Marauders, etc, only rarely gets the kind of damage to sink the barge. I've seen barges with dozens of hits from .50 cals and cannon which are still afloat. For a naval craft with a durability of 1 and ZERO armor, that's a pretty amazing feat.
I never use strafing anymore because of these problems.
Carrier Air Groups shore attacks
There is some kind of problem with the range indicator on carrier air groups that are given a mission to hit a specific base regardless of the type of attack (port, airfield, ground). The net effect of this error is that no matter how many carrier air groups are assigned to attack the target, usually only one will actually go. The vast majority of my strikes now involve a mass of fighters on escort, and one lonely bomber airgroup. Can't do much damage with that. This bug negates the utility and effectiveness of the most powerful units in the game. Combined with the strafing error, carrier air groups are almost useless against shore targets.
Ground Attack by Bombers
There is some kind of bug which prevents all the airgroups that have ground attack missions assigned from participating. I have one base that has something like 12 airgroups with this mission assigned, and only one group actually goes. Again, this means that I cannot rely on airpower to reduce enemy ground troops or help out my own guys. This is an intermittent phenom.
Air supply transport
Please spare me the long historical descriptions of the difficulties of air supply. I am aware of them.
In this game, however, transports aren't good at moving supply around unless within "normal" range of the destination base. This probably isn't a "bug" per se, but given the kinds of efforts that were mounted in the Pacific theater (the Hump, etc.) its a bit irritating. The reason the game works this way is because beyond normal radius, the supply transport plane uses a bit more "supply" than it actually delivers. Given the following two problems, I was hoping that aggressive use of air transport would compensate. I was wrong.
Barge Routine Convoys
I'm probably using these wrong. They don't appear to be much good beyond a 6-8 hex radius. They load the wrong stuff. They decide to load troops on their own initiative. Really bad when a base force gets loaded at a base you are using to support your air efforts against the enemy in a forward area. I tend not to use barges at all. The Barge convoys are supposed to load fuel in every fifth ship, which they do, but it doesn't get used to extend the movement radius of the barge group.
Transport Poverty
I'm really tired of seeing 100 supply transport ships sitting in Pearl with no way to get them committed to my theater. I can't make any serious inroads without the ability to supply the troops. Combined with the Barge problem, I have to rely pretty much on what I started the campaign with to supply my bases. This limits me to two major bases at best. If I mount a large amphib operation, the rest of my bases go into the red because I don't have the transport to supply them while the op is going on. I have literally 40 airgroups sitting back at Brisbane and Noumea simply because I can't supply the base adequately if they get moved to an active forward base (its mid-April, 43).
Das Ist Das Ende
There might be more critical errors that kill the game for other players. This is my list. Because it is my list, I happen to believe these are the most important / critical errors or implementation flaws that need to be addressed. Yes, for those of you who know me, I can even live with the current set of mine rules

When, when o lord gone be our patch?