Back in the good old days, the 1980s and 90s, car audio, like everything else, was simple. Most vehicles had a DIN-, or double-DIN-sized headunit. The headunit would have an AM/FM radio and a cassette or a compact disc player – the truly luxury cars would have both. A small LCD display screen would show the radio frequency or the song number. There would be six preset buttons. Adventurous automakers would integrate CD changer controls which allowed for hours of uninterrupted music, if anyone actually liked the other ten songs those albums.
Today’s headunits are much more than that. CD players are almost extinct. In their place we have USB ports, auxiliary inputs, and blue teeth. AM/FM radio is quickly being replaced by satellite radio. There are apps for Pandora and other such steamers. All of that is displayed on screens that are getting bigger each year, which also display the navigation system. Then there are the camera connections and full integration of phones into the dash. All of this is neatly molded into the dash and controlled from the steering wheel, or knobs or touchpads located by the arm rest. 
All of this makes the simplest audio upgrade, a headunit swap, almost impossible. And frankly, it isn’t desirable, either. Most aftermarket head units never looked right and are often unintuitive and difficult to use. In most cases headunits no longer power the speakers as the use of external amplifiers is increasing. But what if you want a better sound system in your new-ish car?
There are several choices…

Choice number one is to do like the 1990s and take a glance into the Crutchfield catalog. Except that it’s now on online and not monthly in your mail. Plug-in your car make and model, and bam, a list of speakers that will fit your car in every factory opening. They’ll even provide you with painless wire crimping options and mounting brackets. Opt for a powered sub if you’re all about that bass. Crutchfield gives solid directions, too. I’ve done two cars with the products they sell and their accessories, and the installation went mostly well, if a bit longer than anticipated. Their support people are great, too. 
Your second choice is visiting your local professional audio shop. Please ignore any shop that advertises free installation – you get what you pay for. It likely won’t be cheap but a good shop will know all the latest audio trends and products. Chances are that they will tell you that you need more than you think you do but will likely do a damn good job, even if some OEM integrity is lost. They are also likely to push aftermarket head-units on you because it often makes their job easier. Everything has a price and so does a good installation job.

But recently a new option has surfaced. There are several companies out that design systems for specific vehicles. These systems utilize the factory headunit, or infotainment system as it has become known, and all associated factory connections and features. All these systems do take the audio output from the headunit and perform some tuning magic with it. They amplify the signal and properly select the frequency range for each speaker.
Such systems include all new speakers which neatly drop into their factory locations. An external amplifier is mounted in a discrete location, usually under a seat. In addition to the speakers, that amplifier also powers a subwoofer which is placed into the cargo area. All wiring is in specific length and properly terminated, making this a plug-and-prayplay affair. In all, the sound is supposed to be specifically tuned for each model, giving that model the sound of a factory premium audio.
In my research of doing an audio system update to Project 4Runner, I came upon a company called OEM Audio Plus. They make such systems for Toyota and Subaru vehicles. Try as I could, I have yet to see anyone say anything negative about this company. Heck, it was even recommended to me by a Toyota employee. BAVSOUND does something similar but for BMWs and the reviews on that are equally great. 
Have any of you, dear readers, had any experience with such companies and/or such systems? I want to retain my factory headunit despite the fact that it lacks a nav system but the audio quality is killing me.