Quality of life changes:
Don't close the purchase screen after every buy
Warning for unit ending turn in miasma under 30 HP(with move left). Maybe not if fortifying.
Upgrade roads to rails button for workers(quasi automate that just focuses on upgrading the roads)
If really ambitious, i'd like a "connect all cities with roads" button as well, rather than or as well as the currently annoying/picky route to, that just puts a worker or workers on road building duty.
Make the trade route screen MUCH more efficient/obvious( just use the yield icon, not the entire name, to save space. Make it clear what i'm getting and what they're getting. Make it easier to organize. make a "redo" button that doesn't even bring the menu up.).
Miasma more obvious. I've gotten used to it, but I really shouldn't need to, and I still screw up.
Fix the worker automation. I hate manually controlling all my workers, even though it's obviously better than automation. That said I could still usually win in Civ 5 with a couple on automate just to keep it from being something I need to deal with so often. They're especially stupid with the changes to tiles/how things work, so they need a look.
Option to raze the outpost if you have the liberation army perk. This is seriously a downside otherwise in many situations when dealing with the AI, where now I need to decide if i am going to wait for it to become a city(and lose more units) or take a city in a spot where i absolutely don't want it. Thats just awful.
Strategic view.
Easier way to tell if a city has satellites, and to select them(even if i'm missing something, it should really be more obvious. I've lost them in older games by putting them to sleep).
Path to site while avoiding miasma option. I'd see this as a luxury, but often i'm just sending explorers to digs, which is a multi turn no brain thing that I shouldn't need to micro, but since the miasma is an issue(and the dig is covered) i have to try and do all the micro to keep it out. A "take the less efficient but safer route" option would be nice for those of us trying to just have fun and not be hyper competitive.
Fewer clicks/scrolling on spying. This is super tedious for what should be simple. Get me some non crap drop downs and quick clicking.
Balance-
There's so many places they could start, I don't even care, just as long as there's quite a bit. If there isn't anything, there better be a note at the bottom stating they're planning a big one shortly with screenshots or something. It's obvious what's wrong at this point, but fixing it could go a lot of different routes and be quite difficult, so i can accept that, but if they ignore it I will be displeased.
Fleshing out-
See balance. There's a lot that could be done to improve aliens, for example, that wouldn't even need to be DLC level of content, and would make the game a lot better. Again, i see it as a very large project, but they better at least acknowledge this stuff.