I really haven't run into these problems. Enabling Fast Move is the only thing I might do later in the game.
Your system is about twice as good as mine and my laptop handles the game quite well. It really doesn't have anything to do with the graphics. Some tips.
- since your running 4k you don't need anti-aliasing (AA)
- disable VSync
- if your playing the largest map size with only 6 civs and getting to turn 1000 your really asking for it because it means your not reducing the AI's fleets. Play how you want but if your doing nothing but turtling your going to have to sit through the AI pathing for all of their fleets. Fast Move does help this.
- enable fast move this speeds up the turn times a lot.
- use rally points to get around. Set a rally point then use goto command and order ships to automatically send ships to the rally points.
- For icons hiding behind banners you just need to adjust your camera angle.
For the most part many of these things can be remedied.