Yeah, that's the issue with more modern motherboards right there. PCI in and of itself isn't an issue as far as sound card interfaces go, but it's being phased out in the age of PCI-Express.
On top of that, it's said that more modern chipsets don't have native PCI interfaces and use bridge chips, which can cause issues with certain sound cards. I still remember all the infamous reports of Creative cards in the SB Live! days acting up on old VIA chipset motherboards with somewhat quirky PCI implementations. Not sure if other card chipsets of the day, like Aureal's, fared any better.
Other than that, in terms of actual sound fidelity, most modern sound cards are indeed close enough to not warrant switching them out all the time. At that point, any more money spent on audio equipment is best put toward the headphones or speakers and any amplification systems they may need, if the sound card itself isn't sufficient.