I'm fine with the stock system. I don't really want to screw with this that much-- Sounds like the stock mids and highs are just really under powered.
Is that true? Anyone just slap a 4 chan in here?
Since no one else has responded.
You could do that. You will need an amplifier that accepts high level inputs or a line output converter. You will need to tap the outputs of the factory Sony amp. There is no known way to bypass it completely unless you want to lose a bunch of features, like volume control and Sync.
The factory amp has the crossover points for all the speakers hardcoded, so if you want to change speakers you might want to consider some kind of processor or at least a line output converter that has a channel summing feature.
2013+ also have a 3 band equalizer, for low, mid and high. I assume you have played with that...