JMO but I think Apple will either go with a blade SSD for Fusion or a seperate 2.5" bay just for SSD.
If Apple keeps FW, but adds USB 3.0 and Thunderbolt then probably won't get a blade SSD. USB 3.0 means an additional discrete controller on motherboard. Thunderbolt is another controller plus probably a discrete GPU and VRAM on the motherboard too. Conceptually the mSATA slice could be put on a daughter board on a shelf for easier access but not as useful or as straightforward as just incorporating a 2.5" drive tray similar to the 3.5" trays.
Either to be run solely as SSD or as Fusion in the next MacPro, depending on the customer specs. Either way I think we'll still see 4x 3.5" bays so users can add up to 16Tb of internal storage and bigger in the future as HDD sizes grow.
2.5" HDDs will get bigger over time too. Thinner 2TB versions should roll out in the transition between 2013-2014. ( [but even now url]http://www.newegg.com/Product/Product.aspx?Item=N82E16822236348[/url] )
three 2.5" bays SSD , 2TB , 2TB
three 3.5" bays 4TB , 4TB , 4TB
is still 16TB with one of those in a "fusion" set up. Nuking both 5.25" bays it could go in like this ( all transverse mounted like current HDD sleds)
old top 5.25" bay : 2.5" sled 3.5 sled [ the canonical Fusion drive pair configuration]
old lower 5.25" bay : 2.5" sled 2.5 sled [ could get 3 in this row. but two makes it symmetric and easier vibration management. ]
shorten 3.5 row : 3.5" sled 3.5 sled
In notch after two 3.5" drives some more board and vertical space for embedded GPU+VRAM and associated heat/fan subsystem. (or displaced x4 slot because embedded GPU somewhere else displaced it there. )
P.S. why 6? because i think the 4 SAS/SATA links on the C600 ( which are SATA only for C602) are also 6Gb/s. I missed that earlier when looking at Intel's spec sheet. So that makes 6 Gb/s SATA lanes available. Apple would match those up with the storage drive sleds so that all the "same speed". Similar to only offering USB 3.0 sockets on 2012 Macs. If use the others than folks have to know that different sleds have different speeds. ( doable, but not as simple to remember. )