The other limits are really around legacy connectivity and corporate acceptance. I've often described Apple's server history like this. The G4 Xserve gave us a legitimate server. The G5 Xserve let us enter the data center. The Intel Xserve let us build data centers. The Mac mini Server kicked us out of all those data centers.
But corporate data centers is no longer Apple's focus (was it ever?). Small business is where the mini is targeted and this is a really good target. Consider, as you described, you can buy a Mac mini Server for $1500 (figuring a warranty, decent ram config) and a Pegasus for $3000. This gives you are pretty powerful and spacious setup for under $5000. Couple this with the swiss army knife that is OS X Server and you can pretty much do anything you can imagine. From a competition perspective, this means no CALs, no complex setup (although server is still a technical and complex beast, for most users, the required features are easily approachable), and no over buying. With the Xserve, how much of that unit sat there as an idle resource? All those cores for a file server? Sure for those of us doing Podcast Server (another lament), the cores were used. But the traditional deployment of a file server used one core. Wasted hardware.
A limitation is also the form factor and getting traditional IT folks to accept it. Without the buzz words of "dual power," "hot swap," and even "Lights out management," the mini is a low end desktop in server clothing. But the hardware is effectively the same that is in that Dell rack mount server. Intel i7 processor, Intel login board, SSD drives, low power consumption. This is a nice package in a small bundle.
Another is the sluggish 5400 rpm drives. However, since it is a server and most of your data is on external drives (usually), this is often not noticed. I actually will spec the 5400 drives for many deployments to save on cost if I know that I will not need high throughput on the internal volume (no databases, no mail, no small file transaction stuff). I will say however, that the dual drives is what will generate the heat in the unit. So if you are looking at placing this in a confined space with little ventilation, the SSD drives are likely a better option.
And finally, the last gripe I have is the lack of dual Thunderbolt. But I've been able to work around that in most cases. As you mention, perhaps this will be resolved soon.
Now, there are many advantages. Don't get me wrong. I had/have criticism of the Xserve also. I don't think we can every truly be 100% satisfied with any product. But I will say, being one storming the Apple campus with a pitch fork and torch after the Xserve announcement, I have seen the error of my ways. I am a strong supporter of the mini and the movement that Apple is unconsciously driving. We see it everywhere. Low power, better performance. Apple just ended up making a giant leap in the direction instead of baby steps.
Hope this helps. Best of luck with the deployment. You will be fine with a 6 person design shop. Heck, they can be doing nothing but HDR images and this little guy will shuffle those bits without issue. I will admit, 4k video will give it pause. But, hey, I've even done mini servers with 10gigE so, as long as you have the I/O, you are limited only by your imagination.
R-
Apple Consultants Network
Apple Professional Services
Author "Mavericks Server – Foundation Services" :: Exclusively available in Apple's iBooks Store