Westy, I'll reiterate this line:
I think he's tried to emphasize realism where it counts and deemphasized it where it doesn't really matter.
Some of the things you mention matter in air combat, like flaps and dive breaks. Use of these can be critical in an engagement and a superior knowledge of how and when to use them (as well as when not to use them) can be critical to winning an engagement. It may well separate the "men from the boys" in the game.
OTOH, takeoff doesn't fall into this category, really. Not IMO. Yeah, you have to get airborne to fight but the learning curve on that is not very steep or long. And adding difficulty where it doesn't historically belong simply to make it harder is, well, stupid.
Then there are misconceptions, like autotrim. It's a rare historical account indeed that attributes a pilot's victory to his ability to manipulate the trim wheels while hotly engaged. Yeah, it may have happened but generally the trim wasn't touched much during a hot enagement. Maybe a bit of pitch trim, rudder to a significantly lesser extent and aileron probably not at all. So the whole Combat Trim/Manual Trim measure of a man's AH skillz is sorta funny to me.
Don't get me wrong, there's no harm in "selectable" features as long as they don't confer an advantage where there should be none.
Tracer/No Tracer is a good selectable feature. It allows more suprise but at a cost to those not well versed in shooting to begin with.
It's like autopilot. Fighters didn't have what we have. Now, you may choose to sit there and carefully manage your climbout to 10k or whatever, immeresed in the overwhelming realism of it all.

Me, I'll hit a keystroke and go for another beer.

Erg, autotakeoff may well be in TOD. What possible difference could it make? With most folks' level of in-game experience, you should be able to easily get off the ground with these FM's.
Heck, in order to promote "realistic" encounters within the proposed time frames, they may have starts at altitude. Will this turn you off TOD? It wouldn't bother me at all; I didn't come here for the climbout, I came for the fight.