I wasn't trying to be hyper-sensitive to manifold pressure. Originally, I didn't understand why the manifold pressure didn't increase (having experience with a normally aspirated Mooney), but Hitech set me straight and I understand that. Yes, even the Mooney power settings allow for MP greater than RPM under normal flight conditions.
There could still be various issues that aren't modeled today such as prop over speed, over heat permanently causing engine damage, mixture control, manual fuel tank switching (required for planes that didn't feed from all tanks), engine start sequences, etc.
I can kind of see not including mixture as many of the engines had an automatic mixture control. However, starting a large radial engine is not as simple as pushing the E key. You had to prime and crank the engine while counting blades and start when the engine was appropriately primed, otherwise you'd blow a cylinder head or flood it (my dad had great stories of T-28 students blowing cylinder heads on startup). You wouldn't think this important to game play, but it makes a significant difference when trying to get into the air quickly and yet having to do things right to prevent something bad happening to the engine. Vapor lock could be an issue for someone who shuts down for hot padding.
Regarding smoking holes, twins, and feathering, it seems the early P-38 was notorious for losing an engine and needing to feather. I've noticed an impact in dialing back the RPM, but it's impossible to feather in AH3 (unless I've missed something). I do note that there are other threads regarding prop feathering already though.
As far as RPM causing an engine to blow goes, I'm guessing that it would probably only affect normally aspirated engines (causing heat build up faster than normal) unless the turbo has a damaged waste gate.
Manual fuel tank selection is just one of those things. Imagine your drop tank being empty so you punch it. All of a sudden your engine starts to cough because you forgot to manually switch tanks before dropping the DT. Combine this with air restart procedures and suddenly tank selection becomes important. Another related thing is people that put the minimum fuel in the planes and takeoff for a quick fight and never worry about fuel. If you had to remember to manually switch tanks in a fight, you might think twice about having minimal fuel and suddenly having a tank go dry in the middle of a turn fight.
Auto / combat trim is another topic, but right now, I'm not ready to give that up.
I guess the thing I was trying to get to was that a default or auto control that is provided today (auto mixture, engine start, fuel handling, turbo speed selection, trim) should be sub-optimal and there should be manual controls that allow people to improve on the sub-optimal auto behavior by learning how the plane really should work and using those controls to their optimum manual effect.