Some of my wishlist ideas:
* Option to play as a Random sovereign (so you don't know which of the sovereigns you will be until the game starts).
* Option to stop other factions' caravans appearing as monsters (i.e. red squares) on the minimap. I keep looking for all the 'monsters' that are entering my settlements on the map only to find that they're harmless caravans.
* Ability to play the Trogs race as a Kingdom faction. (I'm not sure if this is a bug or if Trogs were intended to be Empire only.) I like the Trogs. 
* Pioneers having a toggleable perimeter guide so you can see which valid city locations (settleable tiles) will be removed if they settle on the current tile. This would help with knowing whether you can fit multiple settlements on those large areas of settleable tiles.
* A High Score table that records the result of all your games similar to the format used in the Civilization series.
* More clarity or visual cues on what types of equipment the unique heroes can use. I recruited Kasst (the Brood Warden) and found out by trial and error what he/she could use. I'm not sure if it was a bug, but my Kasst could use some shields and not others.
* Units/armies move to the vacant tile held by enemies they just defeated immediately after the battle (to prevent the frustration of killing a monster and then watching as an enemy faction collects the loot from the monster's lair before you can move there.)
* Ability to change the order of units in the Army Management box (the box with the nine unit circles). It's really fiddly when you're trying to compare equipment between champions and they are not adjacent in the army. If I select a champion and click "Equip" to see their inventory, and then click the arrows to view the other champions' inventories, I invariably end up on the Details screen of some non-champion unit (because they don't have an Equip screen), which means I have to click "Equip" again when I get to the next champion. If we can't reorder the army units, maybe non-champion units could be a given a blank Equip screen so at least clicking through the entire army doesn't force you to toggle between the Equip and Details screens. (I realise you can use the Trade screen to compare champions' equipment, but that screen doesn't show the champions' stats, so you can't see, for example, which champion would most benefit from extra Dodge or Spell Resist etc.)
* A 'stash' or armoury inventory so that a champion can leave surplus inventory items in a settlement for another champion to collect.
* A non-aggressive way of solving the problem of having your units ejected from another faction's territory. It is annoying when you're trying to cross another faction's land and some turns you are ejected but other turns your trespassing is ignored. Maybe 'free passage' could be purchased through the diplomacy screen or open borders treaties could be negotiated?
* Ability to create custom champion paths/classes. Or maybe an option to take two paths (e.g. Warrior and Assassin) for a certain cost (such as -20% experience). Although I like the inclusion of the skill trees, I feel the old system in FE allowed for greater customisation and variation.
I really like these already mentioned requests:
The ability to change the various faction colors, as they can be hard to differentiate, especially in the early game.
Better contrast so that possible moves are more visible, especially against white background.
When Zone of Control changes, update map at beginning of turn.
I'd also like the collapsible quick view for units, cities, and quests on the left side of the window to act a little differently. If I collapse the city view, for example, I'd like it to stay collapsed, but any cities that need attention will pop back out and still display below. Even on small maps, I end up with more cities than can fit on a single screen, and the scroll functionality is a little quirky.
On the item trading screen, change the "Equip" and "Trade and Equip" buttons to "Equip/Use" and Trade and Equip/Use" so books and other consumable items can be used from the trading screen.
2- Also would like to see UNREST added to the main city info screen...the one at the bottom of your screen which gives a few of important numbers there. Unrest should be on there without me having to go further into the city screen just to find it. If it matters it should be easy to see or perhaps add it to a tool tip when you hover over the city.