While many stock soundcards found in computers are PCI, the fact they use the PCI format has nothing to do with quality or usefulness. Cheap sound cards designed to hit a very low price point are what make stock soundcards unideal. I'll get into the details in a minute.
I've used the M-Audio Delta 1010 PCI soundcards for 5 years now. They sound fine and I consider them to be as good as anything out there in terms of quality (although they have been surpassed in the feature department).
I don't think obsessing about high sample rates and high bit depths is helpful in making recordings unless you have all of your fundamentals covered. I always record at 44.1Khz. My first project in Cubase ended up being 16 bit because I was confused with the new program. It's one of my best sounding projects. I consider myself to be a user of 24 bit, but bit depth is certainly not the most important factor in a recording. As you may know, the louder a recording sounds, the less dynamic range, and the less use of bits.
The real reason to avoid stock soundcards has a lot more to do with their terribly high latency, poor connections, and poor converters.
High latency makes it impossible to monitor using the PC. So, for example, if you were playing midi keyboard real time and triggering samples on your PC using something like Kontakt 2, you'd find that the delay would be too great to pull this off because of the soundcard's latency, or delay time in actually playing the audio.
This is also a dramatic problem when tracking vocals, for example. You'll begin to sing and the cheap, stock soundcard will have to think for a 1/3 a second (worst case). A 333 ms delay is enormous for vocals. You want something more like 5ms (or lower). The only way to do this is with a sound card / audio interface designed for audio recording.
Converters are another issue. An analog signal goes into a sound card but a digital signal goes out of the soundcard and into the computer. This process is called A/D or analog to digital conversion. Crappy converters will negatively impact your sound. While the difference between M-Audio Delta 1010s and super high end Mytek converters (which I dumped a ton of cash on) is actually pretty damn subtle, the difference between a stock soundcard and an audio interface designed for recording is not so subtle.
So, you need to get an audio interface that meets your criteria. You can find all of this in the [URL="http://www.recordingreview.com/soundcard/"]Home Recording Soundcard Wizard[/URL].
However, if you are expecting a dramatic quality difference in going from a $300 soundcard to $1300 soundcard, don't count on it. It will not be dramatic. Generally speaking, the more you pay, the more features you get. You may get more inputs. More outputs. Better routing. Fancier monitor mix features, etc.