I just wanted to respond to these, since they don't exactly match my own experience.
For #2, Mitachurls do fall of later in the game... as leaders. The offensive Mitachurls are still very useful to pair with a Lawachurl leader if you need a lot of damage, while defensive Mitachurls pair very well with Samachurls to keep them protected. A shield that recharges each turn isn't something to be ignored. The only reason to stop using the offensive mitachurls as minions is if you start generating nycto lawachurls, in which case full lawachurl squads become the predominent force.
For #3, I've never experienced the ninja's coming to attack me. While I do generally agree that Inazuma and other distant nations shouldn't send attacking forces at you until you've got some land nearby to attack from, the actual issue here is probably that you've planted a bit too many threat generating buildings in your farm. Which is maybe where the conversation should revolve around. How distant nations should react towards our threat, and how much they should actually be threatened by your actions.
For #5, I don't really see where this is coming from? The trees give you a small amount of their element power each week, which increases the amount of damage you deal and reduces the amount of damage you take from element. Plus, those trees also contribute their element to your farm, letting your slime pools generate slimes of that element. And, at least for anemo, that gives you a consistant supply of large slimes for their rogues without needing to dedicate someone to breeding them.
1: Using Mitachurls as sub-units sounds like a good idea until you realize Whopperflowers exist. Bullet and Binding is a very hard thing to beat compared to the stomp of doom. As far as the shield variant goes, the issue is still one of not having enough of them to really fill out sub-army lists, coupled with the fact that its useless for Chasm/Reef due to the nycto procs needing resistance.
This issue may potentially get
worse with time as well, since Riftwolves are also on the way alongside Vishaps. They pretty much exist for early game pre-elite unit defense and thats it, because the moment elites get involves, mitachurls fall off hard in surviveability.
2: The issue I have with ninjas isn't that they exist, its that there is nothing you can do about them until you get a level three boat and can put defensive units in Inazuma proper. I'm aware of the threat system, it's simply that I have responses for the other nations - not so much with Inazuma.
3: The main issue with the Geo/anemo trees is twofold:
The first is that you want Nycto trees for element generation (Cross that cap and you go bye bye), as well as spawning mass nycto slimes. The geo/anemo trees, while useful to build up some spare element for the cities, aren't as useful in comparison to having that node be a whopper field/slime field/nycto tree. Or even food once the upcoming nerf to food income comes in.
On top of this, you only get one apiece. So if you are desperately in need of anemo or geo to get into the final city states, perhaps they can be useful...but the needed forces to actually beat the final variants mean that you likely have those elements anyway, since you are capable of beating the parts of the map that give you mass element anyway. Getting them after the fact doesn't really feel...useful? As the moment you beat Venti or Morax your element spikes up to the point where you really don't need it anymore. Now, if we had a *cryo* tree, perhaps that would be much more useful due to the peak fight as well as getting whoppers...
The geo tree also has a secondary issue: In order to get it in the first place, you need to kill Azdaha. And if you can beat *him*, you can beat morax. The anemo one at least is early game, but the times where you would actually care about generating geo leave that tree out of reach.
Their lack of use is mostly in a comparative sense, rather than outright. Yes you can get elements from them, but when you line that up against nycto trees and unit generation, it falls off hard. Perhaps if you could generate more, or if you could have it so they won't interfere with generating nycto units via the slime farm, then they would be better, but as it stands right now, there isn't much of a reason to bother with either of them when that slot could be dedicated towards something more useful.