Agree with this totally, as originally the land part was really one of the big things for me. It got me thinking of AoW and how each different team practically had its own terrain type (snow, desert, wasteland etc) - which added to the cosmetics of the whole thing but also influenced mechanics.
It feels really cool when you have the power to warp the land around you to meet your demands, and it also gives you a vested interest in the world itself. Right now the sovereign isn't unique in any capacity, and the land is just a prop for the city building. You don't feel as though you're healing (or warping) a destroyed world any more than you feel as though you're wandering through a desert.
Giving the player (through the sov) more dramatic and variable capabilities to affect the world would greatly increase variability, immerse the player more in the world, increase the feeling of us guiding 'our civ' (which in all honesty is currently nonexistent), and ultimately increase replayability.
I have a couple of suggestions with regards to possible things
1. Magic is obviously the obvious thing here, as I think there's only about 4 or 5 spells that have a lasting effect on terrain, and even these are relatively trivial unless you're using petty tactics like city walling. Implement more permanent (both cosmetic and non) spells that give variability to the terrain. Footstep enchantments (wherever sov walks the ground is turned into x terrain [snow, desert, swamp, etc]), perma-terrain painting spells, varied overland spells with regards to terrain (unit gains +2 mov on swamp, unit gains water walk), and more geo-shaping spells would all help increase the feel that the soverein truly does have the power to shape the world around them.
2. As an addon to this - shards. These things have so much potential and have completely gone to waste, if they are the untapped sources of elemental power in the world it should feel like it. They shouldn't be just sitting out in the open waiting for anyone to just come and slap a brick tower on them, it's ridiculous. Have shards deforming the landscape around them, especially upon release of their elemental powers. An earth shard could be surrounding by spires of stone, or have the land underneath it rising and falling, becoming mountainous and other things. Water shards could be located in the middle of icy tundras or even in swamps or water, periodically flooding the immediate area or freezing things within range. Fire shards could be releasing motes of lava or create a desert around them, scorching anything that attempts to grow; and air shards could have lightning coursing around them, horrible storms and the like.
Tying into this is the idea that controlling these shards is not just a matter of building on them. It should directly involve the sovereign (being one of the most powerful people in the world) and require their attention, and should have benefits and effects (not necessarily positive) that truly are gamechanging - giving players a reason to fight over them. Controlling an earth shard could periodically let you throw up a mountain, or even give a one off ability to summon a mountain range or something upon capture. Water shards could raise the ocean level (would be very difficult to implement) or freeze huge portions of the landscape. They need to feel like unleashing them is an immense (and like I said, gamechanging) occurrence. I've made a quicky tile in about 5 mins (Using the very, very good editor provided) below to show how the current scale doesn't give them the credit they deserve (and that is possible).


As can be seen above this tile is simple to make (literally took me 2 minutes), but also feels much more dramatic than the normal 'untapped' earth shards provided in the basic package. If spell effects and animations were to be added to alter the geology of the land it would really give the impression of something powerful and game altering.
Put simply, I completely agree with the OP and the lack of any ties to the land. There really is no point for the green and black texture change and it doesn't really fit with the feel of the whole kingdom vs. empire thing either. The empire do not by any means feel evil enough to warp the land in such a malign fashion, nor the kingdom el natural enough to bring about trees, flowers, and fairy dust.
All that said I realise it's high past time to make any changes, hopefully this all provides some modding inspiration and gets the devs' attention.
Sorry for the wall of text and I can't wait to play this game!
Paradoxical