Regarding the Academy, though the navigation is screwed up it still gets you somewhat familiar with the keys used for navigation. Long as you can accomplish the objectives (whether you credit for them or not isn't really important) is the important part, getting used to the controls. Unless you're suicidal DON'T do the Flak exam, its unforgiving and general rule of thumb is to avoid attacking planes at all costs and dive to escape em.
Until you're comfortable with everything else I wouldn't think of trying manual targeting (lot of experienced players don't use it either) till last. There's a number of good GUI's out there to help with manual targeting if you really want to tackle that.
The learning curve is steep and harsh, its better to set realism low (like 25% or less) so you can stay alive longer and not have to worry about too many things at once (like fuel consumption or CO2 content) so you can focus on learning how to play. Once you cross the hump and get familiar the rewards are worth the effort, there's no shame in starting out easy to learn the game.
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