Stock speakers didn't sound bad with a new head unit. I replaced my head unit before my speakers since I wanted to make sure it worked right. They had a lot more power and umph, but were still somewhat flat.
I then put in the 4 Pioneer 6x8 4-ways and the damn things are so clear my girlfriend was amazed. I actually only got to do the 2 front speakers only, then about a month later did the rears. The OEM could not keep up with the Pioneers and you could barely hear them. Bass would rattle them.
For the fronts, I used some dynamat around the actual speaker mount, and dynamat spray on the rest of the door. I ran out of spray which is why I waited on the rears. Later I found some cheaper stuff called vbs-1 quiet kote on ebay, which I used on the rear doors along with dynamat around the speaker. I think the quiet kote works way better than the dynamat spray, but has a bit of a smell that lingers for about a month, only while the windows are open. I sprayed the rear doors and the plastic door panels with it, and the rear doors have a very tight bass, no rattles, and amazing clarity all around.
You definitely want a good head unit which you can tweak the sound on. Something that has virtual alignment since our doors aim the speakers into our knees. I know my Kenwood Excelon has it, I believe Alpines do also, my friend has something similar on his $2000 setup.
Different music will require different settings though. I love all types of music, and if I go from R&B to rap to rock to latin, they all require different settings on the enhancements / EQ. (actually it sounds fine to everyone else if I leave it on one setting, but you understand the "audiophile" problem).
I get upset driving any other vehicle now. I was very happy with the job I did even without an amp or a sub, and I did it for $600
