A good list. Here is what I'd like to add or fix:
1) International trade routes - currently you only get a bonus for having a connection between your capital and your cities, however international trade has always been very important, so this should be represented
2) Airports - I don't understand how such a vital building has been left off. This should serve the purpose of both airlifting and trade routes
3) Railroad bonus - currently it seems unfair that the capital doesn't get anything. Perhaps could be in the form of a bulding "Rail Terminus", which gives a production bonus in the capital for each city connected by RR
4) Workboats and embarked units should be stackable with military naval units - this may even be a bug. However I don't understand why totally defenseless units can't be stacked with navy ships
5) There should be a greater progression of embarked unit speed as you get more technology. 4 hex/turn in modern age is just silly
6) Perhaps allow some limited stacking of non-combat units, workers in particular, in order to be able to speed up construction of improvements. This however is debatable. However there should be some an improvement in improvement construction times as you get better technology. It's silly that building a road in modern age takes as long as in stone age.
7) Why no circumnavigation bonus?? This was a very nice touch in Civ4, and I want it back!
8) I really like city states, but would prefer some more variety in city state traits. For example scientific which give a science bonus, and industrious which give a production bonus. This way they could be more varied.
9) Ability to sell off unneeded/too expensive buildings - now that building upkeep can get very expensive, there should be a way to get rid of unwanted ones
10) This is unlikely to be changed, but I really really hate trade posts! The cottage/hamlet/town system in Civ4 was so much better. Trade posts are ugly, and the main strategy now seems to involve trade post spamming everywhere. In Civ4 at least, you could only build cottages on flat terrain. Something should be done about trade posts.
11) I concur with about posters who want more info in the game. List of wonders and Top 5 cities has been in every civ since Civ1. Why not here? Also, where is the Power Graph? I'd also like more transparency about my economy - what is the total upkeep cost in each city, how much each unit costs to maintain, etc. Also in Military Adviser I want to be able to click on a unit and for it to be selected. Currently nothing happens. Perhaps this is a bug. Another thing that I'd like is stats about how many units I've killed, how many cities razed and captured, how many units I lost.
12) Something that has been mentioned before is that the pathing algorithm is too slow. Even a few hexes away it takes a while to calculate the route (not too mention the trespassing issues). This I think is the main reason why the turn times are long - routes have to be calculated many times during a turn. If the algorithm is optimized, then the game will also be much quicker. I don't see a reason why it should be that much slower than the Civ4 algorithm. If anything, the overall graph is simpler - each vertex has 6 edges rather than 8 (you could move in 8 directions from each Civ4 tiles). Of course 1upt should be handled, but I don't see it being such a problem.