I've spent some considerable time looking at payload issues and there are several things that, from a usability standpoint, deserve to be classed as major design flaws.
1) The whole Classify/Declassify idea is badly implemented. It adds unneccessary complexity to what was an already well-designed mission editor.
2) When at the loadout screen before a mission the Classify/Declassify options in the Edit menu are often greyed out, meaning that you can't click on them. This suggests that the options are unavailable to the user. However, one can always press Ctrl-Shift-C or Ctrl-Shift-D to access these features. From a usability standpoint this is terribly bad design: why suggest to the user that an option isn't available when a secret keypress will actually enable access?
3) Maximum weight: Suppose you load an aircraft with weapons such that it's at 99% of maximum takeoff weight. Now increase the quantity of fuel using the slider and a warning message pops up to tell you that you're over max weight. Clicking on OK removes the message but trying to decrease the quantity of fuel results in a new warning message each time the fuel slider is moved down a notch. Again, bad from a design standpoint.
4) Weapon loadout profiles. Suppose you're flying the "Nighty Night" mission in the Su-33 campaign and want to change your loadout. After jumping through hoops to solve the Classify/Declassify issue you'll eventually get to the loadout screen. A default weapon loadout is selected that corresponds to a preset weapon profile. If you want to change even a single weapon you need to define an entirely new loadout profile. This was handled much better in Lock On 1.0x.
I think FC is a great sim, but many of these niggling flaws are reducing my enjoyment of the game significantly.