I feel we do not really talk about the same thing when assessing trade route issues. To be honest my biggest problem right now is with the number of them not because of internal routes but external ones.
Currently the problem comes from the abundance of external routes you can make while still keeping some internal to shape up new cities. I basically use 1 internal for 2 external. This is in my opinion the fastest current way to victory.
I have nothing against the current strength of an internal route but their total number has to be cut down so that you can't make new cities always instantly profitable from a science point of view. Science is only what matters currently unless you go domination. The game basically uses 3 different form of a science victory and more than half of your science will come out of external routes. Even before you start making academies.
Yeah. I suspected that that was the other problem. The output of the routes on Apollo is completely out of whack because of how jacked up the AI is. It's a different manifestation of milking the AI for money at the higher diff settings. Even on Gemini, I have a hard time finding any external for more than 10 bpt at turn 200.