Simao & DJohnson,
I just completely reworked a disgusting Bose system in my Infinity. If you want to talk about complicated messes...this wins.
1-Bose BLOWS. When we ripped out the speakers, we found that there wasn't a single tweeter in the whole vehicle. Bose has now invented the newest audio bullcrap a "Twiddler". I kid you not. This doesn't go as high as tweeters and is definitely not a mid range. They figure that since the amp/head can't reproduce full frequency responses, why try. Thanks Pandora & XM for continued low fidelity.
2-Did I say Bose Blows?
3-The bose amp was terribly underpowered. Even though we had dual subs, there was nothing to push them.
4-Most car USB ports are crap. Not only are you stuck using the built in DAC, you are usually forced to use MP3/MP4 or similar quality. Any of us that have tried to use flash drives in cars will testify to how unreliable this can be.
My friend Chris who is an installation genius did have some solutions. First, Alpine, Rockford and a few others make very nice processors that actually work in line with the factory unit to take out any lame bose equalization to get you full flat frequency repsonse. This is an intense install that is an all day job at a shop and will run $600-$1000. If the processor doesn't do it for you, you can always add an amp or two (or three...). DO NOT SKIMP. Many car audio amps are full of hot air. My Class D Alpine puts out real wattage.
Replacing factory speakers may help but just how much???
Sorry to rant :-)
Go see an aftermarket installer to see what they have to say.