I don't know if this is going to help or confuse you, I hope it helps. I have had subs in the car both ways, factory deck w/ subs, Aftermarket HU with subs, and aftermarket w/ components, Better subs and amp.
My results. . .
The factory headunit is good for the average driver. It was enough for me for about a year or so.
Aftermarket HU - Alpine 9855 - I spent a shiny penny on the HU and was pleasantly suprised. More adjustments, but I blew the factory speakers. . . rattle from hell at all volumes. The amp was a bazooka pro 250 with 2 jl 12w0
Aftermarket HU- Alpine 9855- with sps171a components, Alpine MRV-F545 amp, and 2 jl 10w1v2. Much more clear but not enough midbass for the music I listen to.
My conclusion. . .
Depending on what you listen to, and what you are going to do with the stereo, that should be the deciding factor. Personally, the stock speakers had better mid bass but weren't as clear as the alpines. It was a trade off for me. As soon as I put enough money together I might be going to a component system with 6.5 in woofers, mids and tweeters. If you're not insanely rich and/or you are the average guy, I'd suggest getting the subs with the stock stereo. Then find some people who have different set ups so you can hear the differences. Good luck, I hope I helped and didn't confuse.