Phone volume does not come into play with Android Auto through the head unit.
I did dig around and found a way into an equalizer settings page on the phone and although it was extremely limited in what I could change it did seem to make a noticeable difference. The phone's EQ is crap compared to the car's EQ that is being bypassed though, the car's EQ has the dynamic loudness option which I really like vs the static EQ settings I applied in the phone but its still an improvement so I will take it, finally have a little bass in my music when playing through AA (but only at high volume).
Changing the speakers is a bit of a gamble. The radio was designed to be paired with the speakers it has, you want to watch out for replacement speakers with different impedance that might sound great for a while until the radio fries its amplifier circuits. Of course pairing new speakers with a proper amplifier can remedy that, but its way too much work for something that sounds pretty good to me right off the bat. This stock system beats our Honda and our previous Nissan very easily, but if your previous car had some kind of high-end system from bose or alpine etc then I could see where you might be picky.