As my "main" machine, no. But I have two mini-ITX systems - one in the spare room for grandkids and guests and one in my HTPC. And while assembly in tight quarters is a pain (sometimes with bloody knuckles), once assembled and working, they work great!
Without further research I am wondering if there is any disadvantage to the current ATX boards?
Did you mean "ATX"? ATX (including µATX) motherboards are still larger than ITX (note ITX and mini-ITX are the same) and are still compatible with other ATX Form Factor devices. ITX systems are much more proprietary.
What are peoples opinions?
Sadly, you failed to provide the most critical information needed - what is your intended purpose of this machine? If you plan to integrate this into a home theater system as a PVR, then mini-ITX systems are perfectly suited for that. The better boards have excellent graphics (for displaying digital content from DVDs, BluRays, or cable systems, and more than adequate audio for most users.
If you plan on using this system for school or work projects, an ITX board will probably do fine. If you plan on running the latest 3D animated games at high frame rates, forget it.
As for that particular Gigabyte board, I think it is a nice one, but I don't think - in fact I am quite sure it will not fit inside a C64 case once the CPU and CPU cooler are mounted. And even if you did manage to raise the sides to add more room inside the case, cooling would still be a problem.