There is a big thread about this subject in the Elantra forums. But be aware. Keeping the stock HU and "just adding aftermarket speakers" usually does not get you much. I can't speak to expensive speakers, but in the Elantra thread the goal was to self install and spend about $125 on a pair of coax and a pair of component Infinity speakers. The woofers (same as Sonata) are 6.5 inch.This is what I did as well. I actually like the factory HU, and wanted to keep the interior looking stock. I added an Alpine KTP-445U behind the dash and Alpine components in the doors and dash, and a 10" sub in the trunk with a Sony mono amp attached to the back of the seat.
The sound is many, many times better than stock, and I retained the factory look and functionality.
People who did this experienced better clarity and less muddled bass but lost some bass volume. This is common when going from cheap stock speakers to aftermarket. You get better highs and mids but loose bass.
What cooley did was way above, just swapping some door speakers. He added 2 amps, a sub, speakers, and probably an LOC. A much more complicated and expensive install.
I did exactly what was suggested. I swapped out the door speakers myself and I was not happy with the result. I ended up paying a shop to add an under seat sub, the Alpine amp, and an LOC.
Think about it. If you just swap the speakers you are not adding any power, not adding any additional speakers, not increasing bass response, not changing the HU frequency output. You are just changing the end of a garbage in garbage out chain. Four 6.5 inch speakers and two tweeters can only do so much, no matter how good they are or how much they cost. Some more expensive speakers may "sound" better than the ones that I used but it will not sound as good as adding amps and a sub.