- Lack of really good cases. The Bitfenix Prodigy is worthy of its name, but has serious flaws: it's large enough to be an ATX mid-tower, its PSU bay is ridiculously small, and the loops are entirely unnecessary. Aside from the Prodigy, there are no good Mini-ITX cases. Antec's ISK-300 series has potentially good cooling but is too small to pack any serious graphics firepower, same goes for the Silverstone ML05 and a host of other cases of similar size. The Cooler Master Elite 130 is what the Elite 120 Advanced should have been on release, the Silverstone SG07/08's high cost effectively saddles you with a non-modular PSU, the SG05 has suspect SSD cooling when graphics cards with axial coolers are used (check the AnandTech review), the FT03 Mini has almost no space between the drive tray and the PSU, making cabling a nightmare even with a modular power supply, and no GPU ventilation to speak of, the Lian-Li Q-series mount the power supply in the side, usually resulting in a rat's nest, the Fractal Design Node 304 saddles you with the same small PSU requirement as the Prodigy and removes all forms of cable management, including looping the cables over the PSU, resulting in a rat's nest. Yes, new cases are coming, but that doesn't change the abysmal state of Mini-ITX cases as they are now.
- Lack of expandability on the motherboard. Onboard audio not good enough for you? With Mini-ITX, you either can have integrated graphics and discrete audio, or discrete graphics and integrated audio. No exceptions. Don't mention BTX or DTX, both form factors are deader than disco. The lack of expandability really comes back to haunt you if the onboard audio or the onboard NIC fails. With Micro-ATX and above, you can pay $30 for a budget discrete sound card or NIC card, install, and be back in business after a few days. With Mini-ITX, if either of these happen you are restricted to 1) RMA and wait a general minimum of 2 weeks for a replacement, or 2) shell out up to $200 for an all new motherboard. Alternatively, you can pay top dollar for a Mini-ITX motherboard with a dual NIC. Mini-ITX effectively tells you "your money or your time". How about neither, and build a Micro-ATX PC in a Cooler Master N200 instead?
- Speaking of onboard audio, onboard audio is another weakness of Mini-ITX. Only the high-end LGA 1150 motherboards have the latest ALC 1150 audio codec, with the LGA 1155 motherboards being restricted to ALC 898, which Tech Report's own testing concluded was outperformed even by the budget ASUS Xonar DG discrete sound card. As for the AMD Mini-ITX motherboards, they're lucky if they even get ALC 898. I'm certain people will say "what about the ASUS Maximus VI Impact?" What about it? It's a niche, high-end product, guaranteed to be out of reach of all but the dedicated gamers.
- The fact that having a motherboard form factor that encourages CLC coolers is going to fracture the community further. Reading the comments on AnandTech's HSF and CLC reviews (and reading topics on this very forum) will demonstrate that a divide is already forming between HSF fanboys and CLC fanboys. With the majority of Mini-ITX motherboards not having room for heavy duty CPU cooling aside from CLCs, if Mini-ITX grows, the divide between the fanboys will only get worse.
For all those who've asked on seeing their ATX mid-tower, "Do I really need a PC this big?" after viewing the alternative you'll be asking instead "Do I really want a PC this small?"