By the same token, the trade off for having an internal PCI interface is speed vs. the need to exist in an electrically noisy environment. The good ones cater for this with really good shielding; they cheaper ones can have a higher noise floor than external devices.
Most of the good ones handle this by doing the analog to digital conversion in an external breakout box....
However, the one I'd be avoiding just now would be Firewire--not because there's anything wrong the the technology but, rather, because computer manufacturers are dropping support for it very quickly.
Perversely, you could also argue the opposite. More and more laptops are shipping with Thunderbolt, and you can add a FireWire port to any of those machines with a $30 adapter. So in effect, FireWire is available on more computers than ever before.
And if things go the way I think they will—if Thunderbolt continues to grow in popularity and improves in functionality—then FireWire will probably continue to be compatible with most laptops for at least the next decade.
And even if USB didn't have momentum going for it, it would still be long-term-safe for the same reason that FireWire is. External buses are just easier to support.
On the flip side, internal buses are problematic. At this point, legacy parallel PCI is circling the drain, with fewer and fewer motherboards supporting it, and no cheap way to add it to computers that don't have it. I would avoid parallel-PCI-based hardware. Same goes for CardBus (based on parallel PCI).
And although this may seem counterintuitive now, availability of PCIe is also likely to decline over the next few years. Desktop computer sales are on the decline, as you mentioned. Within a few years (like ten or twelve), desktop computer sales are expected to be lost in the noise. At that point, your only options for PCIe will likely involve expensive breakout boxes.
And ExpressCard is also in decline, because Thunderbolt is "good enough" and takes up less physical space inside the computer.
With that said, both PCIe and ExpressCard are supportable through Thunderbolt adapters that cost about $300 apiece, assuming the card vendor is willing to update the drivers to support it. Given a choice, I would still lean towards external devices, though.