Weapon size modifiers are fine as is.
There are numerous ways to protect your power plant (moving is a good start), and I don't feel any change is necessary, or particularly desirable, other than allowing armored bulkheads to reduce weapon penetration by a modest amount. This would in turn make hull reinforcements useful, as the hull would absorb proportionally more damage.
I feel that submitting and other graceful exits from SC should retain a faster FSD cooldown than forced drops. However, I think masslock should be adjusted a bit, and should apply to hyperspace jumps as well as entering SC. Masslock is too binary at the moment and I like to see it's magnitude depend on range; the closer the distance the more profound the effect, possibly with a greater maximum range (though at low factors) than is currently possible.
I'm fairly indifferent to the logout timer, though detailed connection telemetry needs to be logged and patterns of disconnections during combat needs to flagged, reviewed, and if found to be intentional, punished harshly.
I don't have enough experience with wake scanner to really comment on them at this time.
if you're flying a "space truck" (T9), there's no point in fighting the interdiction - you'll lose no matter what. So you need to find an approach that minimises the risk of interdiction.
Supercruise maneuverability being tied to the normal flight model of the craft never made much sense to me. Personally, I'd like to see SC manuverability and manuverability in normal flight be completely decoupled. All ships should either behave the same in SC, or should have speed and maneuverability based on their FSD vs. their mass.