The motherboard/case/PSU as a unit problem is a real one, but replacing the hard drive isn't that bad. Since you mentioned the SN95G5 and I happen to own one, I'll use that as an example. Since the FDD I ordered was delayed a week in shipping, I ended up installing it after the rest of the components. The steps to install it were simmilar to what would be needed to replace a HDD. First I had to unhook and remove the DVD drive, then unhook the cables on the HDD/FDD and unscrew and remove the drive frame. From there, I had easy access to install the FDD in the frame, then replace the frame, plug everything back in, and reinstall the DVD drive. Replacing the DVD drive was probably the worst part, for reasons I'll get into later, but it really didn't take me more than about 15-20 minutes. I don't really want to replace the CPU in this case, since it'll require a complete removal of all parts and a reinstall, but anything short of that is only annoying, not painful.
The lack of USB ports can be a problem, but for that a USB hub hiding behind the case sounds like the best solution, especially if you aren't using high power draw items and can get away with an unpowered hub.
Note that you can actually save some time on installation since you don't have to connect the front panel ports/switches and you don't have to install the motherboard into the case. Although with the G5 case, this is somewhat offset by the time it takes to line up the CD/DVD drive exactly so that the door open button works (but thats my only real peeve with the case, a BIOS update fixed the only other problem I had). Actually, aside from the DVD drive button, I didn't end up noticing any fiddly little connection problems (at least with my medium-large sized hands, basketball players may have issues). Mostly its just the added time to remove and replace things that you wouldn't normally have to instead of an increase in difficulty getting things to seat or fit right.
If you do end up with an SN95G5, here's some advice:
Don't even bother with the holes for the DVD drive, use the slots. Don't tighten the screws too much, though, because odds are you'll need to fiddle with them. When first booting up, make sure it posts and everything, then try the DVD drive button. When (not if) it doesn't work, take the cover off carefully while its still running (or just leave it off in the first place) and loosen the DVD screws, reposition the drive, and then retighten the screws. Then try the button again. This took me about 3-4 tries since tightening the screws was often enough to move the drive out of position into "permanently pressed" or "not pressed enough". Be careful not to touch any components other than the housing of the DVD drive and the rails of the case while making the adjustments.
You'll also want to update the BIOS to get rid of the network driver not working from a cold boot, but thats easy enough (and since it always seems to come back when you reboot, you don't have to worry about not being able to download the BIOS).
All that being said, a "normal" case does still have some advantages. You won't be able to fit a 2 slot video card in most SFF cases, including the SN95G5. Of course, since the power supply isn't up to powering more than a GT, an Ultra isn't going to work anyways (though my X800XT is doing just fine). You also won't be able to put a sound card and a video capture card in the computer, its one or the other. Given the decent (though not great) onboard sound and the lack of cable in my old college dorm, you might not care about this. You're also a bit limited on RAM, since it only has 2 slots. Of course, a gig of ram is probably plenty for the next couple years. Personally, I don't feel any of these are much of a drawback for me, but make sure they won't be for you.