Basically you want to batch your graphics up into bigger chunks. The graphics card is really best when it's getting hundreds or thousands of lines per object. You really don't need to change the type of graphics object in this case though. Just use nans to combine disjoint strips together.
Your example would look something like this:
nlines = size(faceMx,1);
x = zeros(3,nlines);
y = zeros(3,nlines);
z = zeros(3,nlines);
for i=1:nlines
x(:,i) = [ptMx(faceMx(i,1),1); ptMx(faceMx(i,2),1); nan];
y(:,i) = [ptMx(faceMx(i,1),2); ptMx(faceMx(i,2),2); nan];
z(:,i) = [ptMx(faceMx(i,1),3); ptMx(faceMx(i,2),3); nan];
end
plot3(x(:),y(:),z(:))
I'm assuming here that nlines is actually much larger than 3. As you can see from the performance charts in that blog post, you're not really going to see benefits from this approach until the number of line segments is quite large.
Also, be sure to check out the comments at the end of that blog post. Several readers made very good suggestions on how to improve your graphics performance.
