People on this forum give me s*it all the time for installing a stereo, but I'm glad I did. I have sidepipes and an FE so I need to wear earplugs. But believe it or not, I can still hear the stereo through the earplugs (though you could hardly call the experience audiophile).
I wanted something hidden, but something good. What I chose is a JL Audio HD600/4 amp, which has line-level attenuation, so you can plug an iPod or iPhone directly into it. All you see in the car is a cable exiting where the bulkhead meets the floor, and you plug the phone into that cable. I used a grommet and some nice fabric conduit from McMaster-Carr, so it looks clean.
The JL Audio HD amps have a feature where you can control the volume of the amp using an optional pot, so the install is be clean and doesn't require a head unit. I put the pot on a little custom aluminum bracket I made under the dash, so it is completely hidden but I can reach it easily from the driver's seat. The amp drives 4 JL Audio 5.25" speakers with external crossovers, two in the bulkhead and two in the footboxes. It is far better to use the line-level output on the phone's pin connector, and not the headphone jack, which adds another (very cheap) amp in the chain.
So it works as follows: iPod/iPhone line out (Lightning connector) > Lightning/30-pin adapter > 30-pin to RCA cable > RCA > amp (with line level volume attenuation) > crossovers > speakers.
Look hear on my build log for some pics of the speakers and crossovers (scroll down)
Lippy's ERA #797 build log. My (at the time) ten year-old daughter wired those crossovers, btw.
Let me know if you want more details.