You can get around most of the mess that are integrated head-units with something like the JL audio Twk 88.
http://www.jlaudio.com/twk-88-car-audio-processors-system-tuning-98101
I recently had a system installed in my Tacoma and kept the factory HU. I'm very happy with the sound quality and is a huge improvement over the factory JBL system(the speakers were a joke, 6x9 with magnets the size of a quarter.) Plus it give me different presets for talk radio, music, etc.
Factory HU
Jl Audio Twk 88
Alpine PDV-x9 5 channel amp (4 channels ran to front tweeter/mids for full active system)
Audison AV 6.5
https://www.audison.eu/products/av-6-5/ in front doors/dash
Sundown Audio 10" sub behind rear seats
Nocio 80mil sound deadening in all the doors and back wall
It's a lot more involved than in years past but upgrading your car audio system is still a viable option.