I don't mind the trade route system. It works fairly well now IMO, except for the "magically created" strategic resources from external trade routes.
For me, the biggest problems with the game are:
Non expansion of AI
Its pretty much always so that the AI civs only build three cities (literally!) and then never more. Sometimes one will be four or five, but that's it.
=> An AI that does not expand cannot win the game, its that simple. Not sure if their expansion flavor needs to be turned up or something else, but this MUST change.
Hyperaggressive AI
After building three cities the AI immediately starts building units and then wars for the rest of the game/their existence. It appears there's barely any break at all where they consolidate after a war...instead they jump right into the next one. And the old problem from Civ5 exists here: Why do they start new wars if they have only one or two cities left?
At the same time, I can usually completely avoid any war (except for the wonder war at the end), because I simply expand. I don't even build a big military, only garrison units, but that's apparently enough to deter the AIs.
Tame aliens
IMO this was a big mistake (pun intended) of BE game design. The original game rules were better, aliens that would be non aggressive at first, but would turn on you if you came close to their nests. Now they are totally neutral. If you never fire a shot on them, you will have absolutely no trouble (only the occasional worm/kraken pillaging some improvements). The aliens should be much more aggressive and unforgiving.
I suppose that some of these things are so because I normally only play on the normal difficulty (Vostok). However if you compare this to Civ5 Prince setting, there the AIs expand if they can, and can play peaceful. Other than these things however, I still like the SciFi setting and the great map visuals of BERT. Same with the affinities.