Factory systems have come an extremely long way in the past 7-8 years. What was once an afterthought, now plays an integral part of the interior design. That was the challenge years ago, overcoming an interior that was accoustically crap.
Now, speaker placement is a hundred times better. Some sort of a component set (separate mid-bass driver and tweeter) is very common, at least in the front stage. Paper speakers have been replaced with better material. Sound deadening material is prevelant (I remember pulling out my interior and having to ad my own, lol) Factory head units have decent power, if not external amplification and a sub straight from the factory is growing popular. And now with the video craze (which as an old school sound quality competitor, I still don't get) their catching up with that. I've even seen some cars with a center channel, something that years ago cost me a stupid amount of money to fabricate.
The easiest way to freshen a stock system is to replace the head unit, though now-a-days some factory systems make that hard to do. An aftermarket unit can give you more power (which today's factory speakers can handle) more sound shaping options as well as expandability, and of course fancy displays, lol.
Next would be speakers, now if your car is 1 - 3 years old, the gap between stock and aftermarket has shortened. Obviously you can spend a boat load on high end component sets, but without amplification the difference won't be that noticable to the average joe. One thing I've always been a proponent of is getting rid of any ovular speaker, I can't stand em. There in efficient as all hell and, due to that wear out way to soon. Now their's always been that 6x9 crowd, they love the "bass" response of them, some love them so much the even put them in the rear window of their 84 cutlass. lol. But seriously, for sound quality I've always replaced them with components. A 4x6 dash speaker? Come on, again oval. Replace it with at least a plate. Now you will loose some bass response, but you'll play clearer and crisper and yes, louder. Plus it ready's you for the sub.
A quick tip: Rear speakers are over-rated. Spend your time/money on improving your front stage. That's where your ears are. Seriously, in competition we used the term rear-fill. And that's all it was, something to bridge your front stage and your subs. Some guys I knew didn't even use rear speakers. And this was in a competition for sound quality! How unimportant? In my last install, I had a 6", 4", and a 1" in the doors with a 3 1/2" in the dash for a center channel. My rear fill? just a pair of 5 1/4" components.
Yes, even if you listen to classical, country or rock a sub will help. Now don't be mistaken with the rattling trunk/license plate of the high schooler next to you. I'm talking about an even mix of sound quality. In a perfect world you shouldn't be able to "hear" the sub, its hard to explain. For instance, back in the day, I had 4 JL Audio 12 inch subs with 1200 watts of RMS power. (for those of you audiophiles that have made it this far it was an isobaric enclosure with the JL fiberglass iso-plate ((do they even still make those?)) But, you couldn't get in the car and say "wow you must have a dump load of sub's in the trunk" The mix was even. (I did have a knob on the dash to take care of the punks next to me if needed though, lol)
Understand, sub bass in car audio is your foundation. It takes an interior which is accoustically flawed and kindof even's it out. It gives you an accoustical platform to build everything else on. I'd even argue that just adding a sub to a system like a 8 or a 10inch would be the place to start. It just depends on how much you want to get into it, and how much you want to spend.
I can't really give an all encompassing philosopy here though. Ever car, budget, listening habits, music taste and set of ears is different. If you've got any questions about your specific situation feel free to pm me. You might be able to tell I love to talk about this stuff!