As the image was not displayed in the other thread, I am not sure EXACTLY what you were describing, so the below image is provided for discussion.There will always be situations that can't be solved in an afcad. Indeed it's always a compromise and it doesn't bother me that much because it's a simualtion after all.
For example I am not often very satisfied with the taxi- to taxiway or taxi- to runway connections when surfaces are different (asphalt to concrete or so). It's not easy to get that right and sometimes FS9 behaves unpredictable. I've seen asphalt surfaces even between two directly connected nodes (1000ft apart) while the surface is absolutely set to concrete in the afcad!
Then there are runways that are part asphalt and part concrete or macadam. No way to fix that as far as I know, except for creating custom scenery.
And how about runway markings that are different for both ends? Not possible.
One thing that really annoys me though: when you connect a taxiway to an apron/parking link there's often some taxiway texture missing near the apron (see image). In AFCAD you can see that, but in AFX you can't. It takes some time to tune or find a workaround like an apron underneath the taxiway end. How do you guys cope with that?
[Image not found]
Anyway: it's almost always satisfying at the end, real or not
David

If you look at the left hand "network", some things that stand out are:
1. Intersections with the same surfaces and widths don't have any real surprises.
2. Intersections with different surfaces can produce varying results. Experimentation - including section draw order! - may lead to the desired result.
3. Adding a node away from the intersection may "protect" the intersection in terms of the "proper" or desired display of taxiway surface.
4. Bottom right of the left hand network. When all else fails, in this case, the concrete surface was being displayed on top of the asphalt surface, one can always add a "fake section" whose purpose is solely to generate the desired visual display. This may cause a fault in fault finder but will have no real effect on the afcad other than visually.
Considering the two "star networks":
The top is comprised of 3 non-intersecting taxiways.
The bottom is comprised of 3 intersecting taxiways.
Note the difference in the edge lines.
Bottom right - taxiway and aproway intersections
Apronways have no underlying surface, but add edgelines and that fact becomes visually evident and must be worked around.
Top right - intersections with varying widths.
The leftmost 3 illustrate intersections between 150-100-50 feet taxiways with a 100 foot taxiway. No big deal.
The fourth from the left illustrates the effect of introducing what I call a "stop or protection" node. Note the effect of the node on width at/near that node.
The two rightmost illustrations are intended to show what happens if the intersections are not EXACTLY 90 degree. The widths produced vary "unpredictably" even with minor alignment errors.
I have played and played with stuff like this and highly recommend this type of exercise if you really want to see what is possible and what isn't with afcad design programs. I can't take credit for the exercise itself. It was partially described by David "Opa" Marshall's Tips and Techniques posts/files a while back on avsim. They are all still available and quite a few of the ideas and techniques obviously remain relevant even with the FSX-specific afcad design programs.