Absolutely huge difference. The FiX and TwK really enhance the stock stereo. The whole system with install set me back a little under 5K. Components are warrantied for 2 years and the install is warrantied forever. It is simply amazing what can be done to computer tune your system through the use of JL Audio's Tun software. You can literally modify your tune directly to the driver's seat (90% of my driving) and save over 6 different custom tunes that are easily selectable from the remote knob. They placed the knob and corresponding bass knob in the little "coin holder looking" slot next to the transmission stick, and it looks absolutely factory. Except for the sub box in back, it's absolutely stealth. The only thing I would change is to go ahead and mount the component tweeter on the A pillars to raise the soundstage a little more. But then it wouldn't be quite so stealth.
Like I may have said, I understand the most people would never spend the kind of money I have spent on a sound system. I am about to retire in a year or so and wanted this new Runner to be everything I wanted it to be. I do not want to come off as braggy, I just want people to know that if you want to keep the factory HU and all its controls and have an outstanding system, it can be done. The fact that I'm divorced and don't have to answer to a spouse helps also. Now to the rest of the upgrades.....