Military Armies: it'd be nice to be able to move a division from one army to another, e.g. by drag-and-drop, instead of having to disband it and then reconstitute it inside the other army.
Marketplace production: number to produce input box; has greyed value 1000; greyed values are used in some places elsewhere to hint at the most I can produce; and the text to the right of the box says "max", hinting that this means the same; but I can't make 1000 caravans, skinners or miners (all list 1000 here) due to lack of horses; and I can at most make as many skinners and miners as their respective guild levels. The greyed value could be the actual max I can ask for ! Similar for cotters and number of cottages.
When I'm upgrading something, it shows me present benefit (output rate for basic resources, speed of caravans for market, etc.) and benefit after the next update I could queue, but no longer shows me the benefit I'll be getting when the present upgrade is complete. I not infrequently forget how much that is, which can make it hard to plan (in the interval between starting the upgrade and its completion) what to do next. Similarly for the food that'll be consumed per hour once the current upgrade completes; it'd be nice if these remained on display, in some way (e.g. see next).
The "works in progress" box wastes space - the "queue position" datum could be skipped (start and the progress bar make it clear enough when it's in progress; and, when it isn't, I can only have one queued item, so it's obviously in that position in the queue) and the Action column could be changed to a "To level" column, with just a number in it; if greater than current level, we're upgrading, if less we're demolishing. The freed up space could then be used for other data, or to widen the progress bar.
When City Wall is upgrading, its "Upgrade Further" box over-lies the picture of the city wall, such that the column for wood, and those to the left of it, are largely unreadable. It may be relevant that my browser window is 986 by 1507; however, I tried making it wider, and this didn't help. I have the browser zoomed to 110%, but changing zoom level didn't make any difference, either.
Demolition is handled clumsily. If a demolition is in progress and I queue some building, the demolition is shown in the "next in queue" space in both the city view and the Next Events box, with the building in the "current" space, albeit the demolition is what's got a moving slider. When the demolition is complete (in this case, from level 13 down to level 12), the Notifications tab says: "Storehouse L12 completed", which isn't really a faithful account of events !
Protected by Vault: having a separate column for this is kinda icky; it's not a resource type in its own right. How about: the existing first five columns for basic resources, blue/green on a beige background -
but the bottom portion of the beige background is pink, indicating how much of the columns is protected. The pink is an even depth "behind" the five columns, across their width and a little to the right; the space for the present sixth column is now free; from the right end of the top of the pink to a convenient height beside the labels, the pink fans out or in to meet its label text and show its meaning - along the lines of (sorry the image is kinda messy - Gimp and I don't understand each other):

Various of the top-bar's primary icons have green, purplish and sometimes red boxes at their tops, indicating stuff to pay attention to, that you can find out about from the pages to which they give you access. It would be nice to use the same idiom for (at least) quests on the world map icon; e.g. use green for number of New quests available for the currently-selected town; maybe use purplish for new herald articles, release notes, tournament announcements, red for when the daily freebie is available for collection.
Global Rankings -- I may be odd, but a page on which I recognise no names, that's part of a vast list of insanely many pages (currently 742), isn't really of much interest. It's the detail I might take an interest in sometimes, but I'd sooner at least start out on a summary, e.g. a simple bar chart or histogram showing my positions in the nine rankings, out of the total number of players, with my numbers of points in each, something like:
Overall .....|....... 2897470 Quest ..|.......... 1309 Population .....|....... 1964 Attack .....|....... 118 Defense ...|......... 0 Diplomacy ...|......... 4 Trade ..|.......... 0 Research ......|...... 92550 Magic ......|...... 87
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Then each ranking-name (Overall, &c.) can be a link to the page currently given. It may make sense to display both graphic and numeric values for both position relative to the population of players and score (out of some sensible max, e.g. that of the highest player, in the given category), where the above uses graphic for the former and numeric for the latter. It may make sense to truncate a bar in the diagram at the point where all players to the right have zero, as for Defense and Trade above; or grey out the part of the bar that corresponds to the vast mass of players with a zero score.