Despite my overall satisfaction with WitP-AE, my top 4 would be:
The first two are pet peeves that don't really affect game play;
1 - When you combine multiple small units into a large one, as in recombining a division, and later split it, I would love to see it split into it's original units (rather than /A, /B, /C)
2 - An easy way to find all ships of a particular class. (Unless there is an easy way I've missed.) I'm always doing this when trying to set up convoys, looking to upgrade ships of the same class, etc. Right now, I filter by endurance, speed, etc.
The last two lead to, what I think is unrealistic strategies, that I'm guilty of using.
3 - Higher fuel consumption for CV TFs (and perhaps others) in certain conditions:
Who needs oilers! Just fill up at Pearl or Truk and cruise around for weeks. At least this is what I do vs the AI. In Lundstrom's Black Shoe Carrier Admiral I was amazed at how quickly fuel was used up when CVs were conducting a high rate of operations such as when supporting the Guadalcanal landing, mainly from having to steam at high speed into the wind to launch and recover. For certain patterns of flight operations, fuel consumption should sky rocket and force me to refuel more often.
4 - More terrain limitations for motorized units:
Armoured divisions over the Kokoda Trail / or pushing multiple through the Burmese jungle to Bangkok should is too easy now. I'ld through into this category the ease of operating in the Aleutians during winter.