You are correct that two x16 lanes will give the best performance. However, all multi GPU will only ever have the need for dual x8 lanes, for now. The performance difference between two x16 lanes and two x8 lanes is very minimal, at best. Something like 1600 CL9 RAM vs 1866 CL9 RAM.
And motherboards with dual x16 lanes are actually quite expensive, and are usually associated with Extreme series CPUs (Two x8 lanes on an AMD board is quite rare, so talking about Intel here), so along with getting an expensive extreme series CPU, you'll need that expensive extreme series motherboard.
Most boards will support dual x8 lanes. A x16/x8 board is.. nonexistent? Because I believe if you're using SLI, it'll be using dual x8 lanes.