Truth of the fact is, with Thunderbolt,especially as it improves in speed, there's not much use for internal PCI-e and Hard Drives.
I do not see speed as the issue. The problem is the more things you have outside of the case the more unwieldy your system becomes. More data cables. More power cables (and power supplies). More independent devices that could have cooling issues. If I plug a 3.5 into a tower everything is there. If I put it in an external case suddenly my real world desktop becomes more of a mess.
Apple is a bit schizophrenic on this point. They want to reduce clutter, fine. At the same time they want to reduce the ability to hide that 'clutter'. The need for multiple 3.5 drives (for example) in a MP will not go down ... the question is will they be 'out of sight, out of mind' or will they add yet another external device?
In theory there are only 3 things that should be outside of a good tower. The keyboard, a mouse (or other pointing device), and your monitor. Production drives would go inside, although there would be a data port of some sort so you can hook up a drive to back up to if it is unwieldy to open the case for that.
The iMac follows this concept: using wifi, blutooth for your keyboard and mouse, not using using CDs/DVDs/Blu-Rays and ignoring backups you only need a power cable. They also made it so most expansion would need to be outside of the case, defeating the whole point of a clean design.
I would rather have a MP and put all my stuff that should be internal in one box. Who cares if it makes the box heavier? If that was my criterion I would be using a laptop.