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I have designed and installed many custom stereo systems in dozens of homes and vehicles. IMHO: no factory audio system will ever compare with the quality that can be obtained by installing your own custom after-market solution, however many factory systems will be a good value for the money especially if you don't pay the MSRP price.
My Tundra DC Limited has the NAV package with 440w 10-speaker JBL sound and it is awesome. Very clean and clear, no real distortion until you get way above the normal levels even when you like it loud and thumping. A big plus is that it is factory installed and all components are nearly invisible yet it has a powerful sound. If you want to install your own system be prepared for many hours of disassembly and reassembly and you will have to spend at least as much if not more than the factory discount price to get a system which sounds better (including head unit, speakers, amp, wiring kit, mounting kit, etc.)
Sure, the highs and mids aren't pristine on any factory install but in reality this is a waste of money since road noise will cancel out even the best high-mid quality so no sense going overboard unless you plan to sit in your driveway and listen. You can install expensive sound damping materials to help but no need for this unless you are an audiophile and plan to go to competitions, in which case you wouldn't have even asked about the JBL system in the first place.