I think the design works pretty well as it is but it generates a fair bit of noise when the fan is going. Maybe a Mac Pro-like cylinder would work out ok. It wouldn't need a triangular heatsink but they could have the PSU at the base, a single 2.5" HDD in the middle so the cylinder diameter would be just larger than the width of a 2.5" HDD - just under 3" and the height would be just larger than the length - around 4". I'm not sure if the 3" fan would be as quiet as the Mac Pro but that design should have better airflow. They can supplement the internal HDD with an optional SSD to keep the price down. With both HDD and SSD, it would make a Fusion drive and there can be an SSD on its own.
A cylinder desogned Mini has a lot of potential in this regards. Make it half the size of the Pro and you would still have plenty of room for a strongly performing desktop.
When HDDs eventually go away altogether, the design can be shortened.
However that being said I hting it would be easy to build a Mini in a cylinder type housing with room for a blade SSD and a standard format hard drive "bay". Todays high integràtion chips would allow for the CPU card to support memory and a SSD mezzanine on one side of a heat sink with the bad side a mounting point for a "disk". In otherwords imagine a machine like the Pro but instead of a triangle heat sink it has hollow slab in the center, one side for the CPU board and one side for the option. These days you could easily do such a machine in a 3-4" diameter tube.
Note I used the word expansion there, the latest HD standards support both PCI and SATA ports. The PCI ports might be a way to offer optional expansion in the form of a "disk" format device.
I don't know why they skipped the Haswell chips in the Mini. A lack of refreshes typically points to something being EOL but it could still be the thing about moving manufacturing to the US. They also couldn't update it before October 2013 as they needed dual-core processors for the low-end. The 13" rMBP actually moved to ULT dual-cores.
iOS is a lightweight OS that works with very small amounts of memory (under 1GB and no virtual memory). This is great for servers and virtualization. They can make an x86 version of iOS server to run on generic hardware too. Most of the software intended to be run on it will be compiled for it anyway. Apple could then make a low-cost personal server product or put an ARM chip into the Airport to use as a personal server.
Actually an ARM based server is a good idea. However I think Apple is scared of the server market.