The vast majority of the problems listed here are things I fix in 'SM Mode' at the start of each game. Want more Naval Academies? Use 'SM Mods' on the F2 'Population & Production' screen to get them, and pay for them however you choose (Direct removal of the appropriate amount of minerals, removal of other buildings, upping the Empire's military level, etc.) Want forty years of officer corps? Use the 'Replace All' button on the F4 'Officer Corps' window to generate a brand new crop (a dialog box asks you how many years' worth of officers to create; expect it to take a couple minutes for 200-300 officers). Want a decent Governor, not a politically reliable appointee? Use the 'Promote' and/or 'Demote' buttons. Want a decent Governor, in a pre 3.2 game? Exit, go to Game Options, turn off realistic promotions, save the game, select the game, use the 'Promote' and/or 'Demote' buttons, exit, go to Game Options, turn back on realistic promotions, save the game, select the game. Prior to version 3.3 you can 'open up space' at the top of your officer corps by assigning political appointees and other high-ranking 'undesirables' to 'managerial' teams - teams you uhave no intention of using.
P.S.: Those of you reporting double the number of expected officers check the 'Training Level' vaue on the Ctrl-F2 'Races' window. For the 'Player Race' Govt. Type this should be 1, but if you chose (or were randomly assigned) another government type this might be 2, and thus academies will generate double the number of officers & crew.