I'm not sure the Mac Mini really needs to be like the Mac Pro; the Mac Pro is a pro product, so Apple won't want the Mac Mini to look the same anyway. But more importantly, the Mac Mini only has a single processor to cool, unlike the Mac Pro which has three very powerful ones, so the Mac Mini doesn't need anywhere near the same kind of cooling.
That said, I could see the Mac Mini becoming rounder or even circular, but probably keeping the top closed with a blower style fan. Hopefully a bigger fan so it can run quieter under load; assuming the Mac Mini doesn't get shorter it should actually have a decent amount of room, as I expect we'll lose the second drive bay in favour of PCIe storage options. Soldered RAM seems possible, though of course I'm hoping not but if they decide to prioritise cool/silent running then it may happen if it means freeing up space.
The alternative is that we may even see the fan disappear entirely, in favour of the case itself becoming a full-blown heatsink, which could work out well if Apple waits for Broadwell chips and they run as efficiently as Intel is promising.
I'm just hoping Apple doesn't reduce the width/depth of the Mac Mini too much, as I'd like it to remain VESA mountable. I also much prefer the flatter look to the IMO very ugly tall airport extreme.