I have never played AA42, but there seem to be some changes that would favor the axis.
1. The UK battleship off Gibraltar is now a cruiser instead, so this frees up at least 1 German fighter on turn 1 to do something else. Heck, under certain circumstances, it may even be acceptable to skip this battle (say with bad USSR dice on turn one, making a full eastern assault desirable).
2. New transport casualty rules seem like they would favor the Axis. UK and USA have to build more protection for their transports. Japan is affected by this too somewhat, but usually USSR and UK are not in a position to snipe much at Japan’s, so I think Japan is affected less than than the Allies. Given a full KJF from the USA, of course this would come into play, but I assume KGF is still the more common strategy.
So it seems in theory, the game should not favor Allies as much, but maybe I am missing something, not having played it yet!
Edit: Just thought of something - the German Med fleet is affected by the transport casualty rule pretty badly too, so who knows!