i think trade routes should be established between civs not particular cities, and they should be permanent but with an option to reassign.
In practice, trade routes are established between Civs, but they're made effective with a physical trade route between cities. Which I think is the right way to do it.
As for permanent trade routes, the problem with those is that you often get too involved in other managerial and strategic activities. So there's a risk of the player not being able to remember to reassign them in good time, if the option doesn't pop-out from time to time.
there could be a notification when a better option becomes available
The road mechanics are going to be very different, so it's hard to speculate.
Do we even know that builders are going to be the units that build roads later? (Early the roads auto-appear with trade)
In the E3 video, the trade route appears to have a combat strength of 6, which is weaker than a scout, but at least not completely defenseless. I can imagine that there may be technologies or civics that increase this value.I will say having some ability to invest extra in your trade route to give them some protection would be a good thing, though. Either with devoting an actual unit or just paying an extra fee to upgrade the caravan itself somehow.