Thanks for this insight, this is really useful.

As someone who studied trade routes in history during my university degree, I am always bothered when I see obviously non-sensical trade routes on maps sometimes (long straight paths across desolate plains and so). While I am not telling that fantasy map must be super realistic, I always find it nice when it is following some inner logic.
For creating pseudo-historical maps I have my personal rule of thumb when placing major trade routes (and roads generally):
1) if possible, follow the rivers (in ancient/medieval period transport by boat is nearly in all cases easier and faster then on dirt roads)
2) easiest, not shortest path between centers (around the desert, not through it)
3) think about the logic behind the road/route/path and what is the economy behind (trade route will go through one urban center to another, because they want to sell stuff, on other hand modern-era road for quickly moving armies could be quite straight and actually be passing around inhabited point to avoid being clogged by civilians/refugees)