The title is pretty self explanatory.
P.S. I understand that it depends on the price, but is it true generally?
Most modern mini-ITX boards would have as much features as other standard sized mainstream boards. But "what do you need your next PC for" has to be answered first.
None of them support Crossfire or SLI (Obviously) and they only have duel channels. So yes kinda...
I've seen some nice ITX boards with a lot of features but none of them have those. So kinda it does limit you but only kinda. Also if you do want the extras you do have to pay a bit more. You can't just buy an extra card and throw it into a PCIe slot. So that's also something to consider. When it comes down to picking your parts it really is all about what you need... But they do limit your options for the future to some degree...
Its definately important to consider what you want to do in future. Remember it can be advantageous to just use 1 graphics card as you don't get vsync issues like you would in Crossfire. You can stick to using 1 very powerful graphics card. Remember not all of these mini ITX boards will come with pci-e x16 so be sure to pick the right one. There are sometimes less SATA ports on these mini ITX boards though. I have the MSI B75IA-E33 motherboard for my HTPC and its great for its size and price.