That is actually my biggest gripe with the current model Mac Pro ("trash can"). If I'm using a desktop computer, I want everything to be enclosed in a single unit as much as possible. I have and still use the previous model of Mac Pro ("cheese grater"), and I have six internal hard drives, maxed out RAM, and several PCI cards. None of that is possible with any current model Mac except maybe the RAM.

For disks USB is alright but it's always been kinda flaky compared to SATA or PATA. The only external port I've used for external HDs that's been as stable as internal connections was FireWire, which unfortunately never really took off.

I could definitely see why professionals or otherwise demanding users might prefer internal disks over external ones.

true. of course, a lot of the external SSDs on the market are bound by SATA interface like speeds anyway (even if they have fast external ports). so they won't be as fast as the internal flash memory in, say, a new iMac. the comparison is roughly: 500 MB/s vs 1700 MB/s

http://www.apple.com/imac/performance/

an alternative to the garden variety external SSD would be an external PCI-E card housing (e.g. sonnet or akitio) connected through a Thunderbolt cable. now that's a lot faster.

but, for that we buy an external housing in addition to the actual storage that goes into the housing. so this is more expensive than computers which let us install a PCI-E storage card directly inside the case. which Macs don't let us do easily or at all.

Except when anything slightly unexpected happens (sleep etc), your external drive is not cleanly unmounted and you risk heavy data loss, whereas internal drives are always handled properly.