I agree that the current case is not "perfect", and it's really due for a redesign. However, with an internal SATA card, you can easily stuff 8 drives in the Mac Pro case, as long as at least two are 2.5" drives and you relocate the DVD drive to an external enclosure. Make the SATA card 6G and you get a benefit there too over the stock SATA setup.
You can also do as I've done and get an eSATA card and/or USB3, and string external enclosures to the Mac Pro to your heart's content.
I believe that there's a basic divergence in the customer base who's interested in a tower style configuration, at least for purposes of the question of
"How many drives can I stuff into it?"
The first consumer group is
... and apologies in advance for a sprinkling of hyperbola to magnify the point ...but we've all been guity of being this very person at some point ... the "Penny Pinchers" who never really ever retires their older, smaller hard drives. This user claims a need for more than 4 bays becaue they have installed a 1TB, 750GB, 500GB, 250GB plus the original 160GB drive that the Mac came with ... all still running.
The second consumer group is more typically someone who needs tons of storage, particularly with robust data repository attributes. In their view, a single spindle backed up by a single spindle "Time Machine" is simply an unacceptable risk ... even before us bothering to check to see if the current 3TB size limit of an individual HDD is even adequate. Nothing less than a couple of RAIDs will suffice for their data management vision, and each RAID that they require promptly doubles the numbers of spindles needed.
To either/both groups, there can also quite easily be a need for speed, which is where 2.5" SSDs come into play as well.
To try to satisfy 'most', then design challenge would probably entail a system that is designed to accomodate 4 * SSDs + 4 * 3.5" HDDs. That can be done with today's Mac Pro design, although not as an Apple OEM.
FWIW, another alternative that would IMO be quite interesting would be to borrow from the Apple parts bin the SSD "sticks" from the MacBook Air...and have them plugged into the motherboard almost like RAM to be used as the Mac Pro's boot partition. Unfortunately, I don't think that this is particularly lkely to see from Apple (...since the right way to do it would entail splitting off the user directories onto another logical drive, which OS X can be made to do, but isn't a default configuration...), even though this is a straightforward approach to boost hardware performance that they could then pick up in their product marketing.
-hh