Many people have been focused on big things when looking what's wrong in Elemental. This time, I'll focus on small things that can make game annoying, and if fixed can make gameplay more fluent.
Usually in games like this, some things don't need reinventing the wheel, and and already established conventions are the way things are done. And for good reason.
Let's start with movement mechanics and anything related to that.
In Civ, every unit has Wait, Sentry and Fortify order.
Wait is something similar to Elemental TAB for cycling units, basically, you go to the next active unit without skipping turn for the current one.
Sentry is a way to get unit out of the cycling loop. It means don't bother with me anyone, and only make me active if something happens near me (like passing enemy unit).
Fortify exempt just giving defense bonus also means, I'm here to stay, don't cycle me ever, exempt if I get unfortified manually. It's also used as a way to park units in cities.
In Elemental there is guard duty which I guess is something that is supposed to be similar to sentry or fortify from Civ, but the big issue with it is that is does not remove unit from cycling loop. Every turn unit you don't want to move anymore will get cycled to, even if this order is active. It doesn't even switch to next unit after order is issued, you need to manually press TAB afterward. This is especially annoying for ships, when you want to "park them", and not do anything with them for some time. At least, land units can be added to cities, which will remove them from the unit cycling loop, but nothing similar exists for ships. Fortify order from elemental behaves exactly same as guard, so is no help there either.
Another thing to mention here is that point of unit cycling is to get to the units you want to move, not to those you don't want. So why being forced to cycle through Caravan every single turn in the game. You can't do anything with them, nor you want to do anything with them after have established routes. Just removing them from unit cycling loop with remove at least 50% of late game tedium (tip: make special caravan cycling button/key, if really needed, or better: make separate trading screen/table for that).
Another point I want to make is "go to" order. In games like Civ, after order is issued, next turn when that unit gets to act it moves immediately. In Elemental that is not true. In fact, you can still cycle true units that have go to orders, which kinda loses the point, since the point of go to is that unit moves on its own, as something that reduce micromanagement, when you don't want to get prompted every turn should you move it manually or not. Also, advantage of having it move immediately when its turn is, is that if any moment points are left, player is back in control and can spend them manually, or issue new go to order. In Elemental go to, on the other hand, it is done on the end turn only, and if destination is too close to spend all movement points, remaining ones will get lost.
Now, when are we at losing movement points, Elemental uses strange mechanic of auto-stacking units "on contact", without having any mechanic to unstack them when on same tile (or manually changing stack composition if there is more then 12 units in tile). What is really bad with this is that is also reduces movement points of units "on contact", to the lower value. So, if two units want to pass each other, and one has 4 movement and another 2, the moment the 2-move unit enters the tile of 4-movement units the other one will have its movement in turn reduced to 1 or 1.5 (1 if 4-move units stands at empty tile, 1.5 if it is on road tile). Often, when units enter same tile, you don't want them to stack, nor to one of them to lose movement points due to other. So stacking should be done explicitly, and not be automatic.
Something similar can be said when passing cities, usually you want to move between cities, not stay in them. So unit entering city should not "lose focus", and also not get its movement points reduced similar to the case above (when auto-joining stacks), at least not without explicit guard order or something.
There are some weird combos you can get here. Let's say there is city and two units that want to pass true it, one with 2 and one with 4 movement. The guy with 2 movement is two tiles away, so uses 1 point to get near city and another to enter. Now it has 0 movement points, and can exit the city (since it takes no movement). Now, all units in garrison have 0 movement points, due to that "auto-stacking stealing movement points" mechanic game uses. After this, if 4-move points enter the city, it will lose all movement points, since defenders have 0 movement points, and same stacking mechanic is applied. So the only optimal way to go through the city is to eject defenders to some third tile, move 2-move units in and out, and them 4-move units in-and out, and then bring back defenders. Very annoying thing to do manually. And counter-intuitive.
Ok, that's all from me now. I hope I made some good points. In conclusion, I'll say this again: this is not first land 4X game, and there is no need to reinvent the wheel for some basic stuff. And for good reason. Fixing things like these could make game much more fluent, and remove most of the tedium from late game.
P.S.
I just remembered that enemy caravans can block the roads for your troops. When not in war they should really be able to share same tile as your own units, so they don't block road choke-points, which is very annoying. When war starts, if sharing tile is an issue, just auto-eject them to nearest unoccupied space.