It's mainly about sound. With ISA you have a lot more options. If you're used to Windows, the difference between sound cards are minimal, at most how noise-free they are (SNR), how much CPU they use and whether they have fancy positional audio features (A3D, EAX), and hardware support for the latter also went out the door with Vista. In DOS cards really sound different, so a single PCI card pretending to be a Sound Blaster won't necessarily sound like what you may remember or want.
Agree that compatibility is not likely to be your biggest problem- pretty much everything will at least make AdLib or SoundBlaster sound, even if it's not perfect, and the games that have trouble with the TSR programs needed to emulate an ISA sound card on PCI (or the conventional memory they eat if you aren't allowed to use EMM386 or even HIMEM) will definitely fail due to CPU speed as well.
Bottom line: what are "some DOS games"?
If it's late DOS mid to late 1990s games, any PCI card with DOS support is good enough to be playable if not perfect. If it's older than that, you want a slower system anyway.