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It would help to know what kind of $$$ you're looking to spend.
As for me, I'm running the stock head unit with an aftermarket amp + aftermarket sub with a custom enclosure. Kept the ML speakers because it still sounds nice.
If you provide the ML system with quality sounds they do sound very nice! Adding a sub via a line converted to add a sub does trick because the OEM sub SUCKS!
Im using an LC2i line converter and running a Zed Minotaur pushing a Morel Ultimo mounted in a 4080 box. I have my music apps set to provide the highest quality and running to the ML system via a Vaistech ivic.
It fits nicely against the back seat and it is very low profile and light....and if you want more thump, just add 2. Planning on adding one in the next month or so....