The biggest thing that I wish were more accessible within the mini-ITX form factor is 10Gbps ethernet. Maybe with thunderbolt it could now exist as an external dongle, with the right motherboard, but internally there's few options today. Very few mini-ITX boards offer anything faster than 1Gbps, and of course have no additional PCI-E slots (despite the chipset bandwidth being more than ample).
I believe Intel's enthusiast Alder Lake chipset (x690 IIRC) specifies 2.5Gbps ethernet as minimum spec, which is nice; but it ain't 10Gbps. This is something that Mac just plain-out does better, no argument; the Mac Mini has had 10Gbps ethernet as an option for years.