#1 City Improvements
Houses are the biggest issue I run into. No matter what I do, my city ends up at a standstill requiring reorganization to fit more houses.
Why not make houses automatic? The city grows based off your surplus food and houses become sort of a pleasant visual buffer zone between the city improvements. This makes the city improvements spaced out and visually, a little bit nicer, with little huts and houses in between them. This might require rebalancing of city space per city level, but in the end, it eliminates one of the tedious aspects of city building right now.
Either that, or I would go with housing area instead of just a single hut or house. And make it upgradeable, so that if I have huts and research villas, I can improve my four tile housing district to the next level, rather than demolish and rebuild.
Tooltips and new requirements. I may have missed it, but when you get archery, you can design an archer unit and never be able to build it because nothing showed you the archery range is required. Maybe the yielding technology could be displayed like this:
>New Ability: Ranged Weapons
->New Improvement: Archery Range
-->New Item: Yew Shortbow
This shows I gain the ability for Ranged Weapons, which lets me build an Archery Range so I can make Shortbows. An example of technology info that doesn't have reqs:
>New Item: Shortsword
The Longsword here doesn't require the shortsword to be made. The only reason I find something like this would be useful is when Techs give us multiple rewards, but we have to build/use one reward before the others are available.
#4 NON-HUD Information
I'm not sure if this is planned, but I'd like to see the actual City tile grow. It always looks like a wooden fort. Will it age into a keep, and then a stone castle, and then an ivory tower? (for example)
If the houses were automatic, they would also grow out with the city. This growth should also be on the cloth map. Similar to Master of Magic, this would be comparing a hamlet to a city - the city stretches a bit further and has a level of magnificence to it. This instantly distincts the difference between a low population city and a high-pop city, which is my point. Population is hidden in the bottom corner of the screen. It should be more obvious (but unless the hardcore HUD is on, no numbers on the map!).
#5 Visual Distinctions between Factions.
First thought on this: Emblems. Crests. These should be displayed somehow on units. Your mentioning of flags gave me an idea you used in Gal Civ 2. You had components that gave a buff to an entire Fleet. Why not have Herald's or Flagbearers that can grant an entire army an ability? With magic, you could even make enchanted Standards. This could be fun, but I guess in the end, it'd end up being doable in the modding editors. It would just be nice to see the Crests/Emblems more obvious on units.
A different building or 2 per faction wouldn't be bad, or even individual gear. I'll have to come up with something specific.
I need to brush up on the factions a bit more, but a special ability for Pioneers might be nice, as well. An example would be, one faction is from the mountains and their Pioneers can build tunnels through mountain ranges. Another is a faction of exceptional traders, perhaps their Pioneers can upgrade roads in highways. Maybe a warlike factions can have Pioneers build Forts outside city limits, or walls, for a forward defensive position.
#6 Other types of World Resources
Off shore resources would be a nice twist to a fantasy game.
Turtle Mounts,Coral Reefs, or Underwater Shards?
What about tile specific resources? Maybe a Goldenwood thicket in a cluster of forests, a Waterfall on a river tile (some kind of mill improvement?) or something to that effect.
It would be interesting if there were Essence Fonts. Areas naturally saturated with Essence that can quicken mana regeneration for champions.
I think animals can play a big part here. I saw someone recommend that a cattle farm have a slaughterhouse and a tannery for bonus food and materials versus a mill. Well, in order to have cattle, you need cows! That could be a resource. Alternative mounts could have a great presence here, but they need to be different from horses. Raptors have an extra attack, Elephants grant more defense, and Turtles (mentioned above) can swim? Having any of those available could greatly alter tactics.