I'm at chapter 5 with Yuela's route and after reforging her sword it doesn't seem fun anymore. I'm a feeling a bit like Wil, that my job is done. I don't like how the story develops either. It seems like those crazy guys in Disnafrody are planning an invasion into Mikelty and I don't want to be part of a war like that. So I wonder, are my suspicions correct or does the story develop in a different way? I'm thinking about starting over and going with Serawi's route instead but heard the story in that was a bit lame so I'm very torn right now. Don't be afraid to post spoilers but if you can avoid them it's better.

There's gona be a war.
But it has an happy ending with most cast ending up alive. There will be a notice at the end that "many alchemists died for the sake of this war". But nobody you've interacted with will die.
Well the actual "war" won't start until chapter 8 or 9. And chapter 9 its the last one anyway.

Playing tough one route and reaching its end. You can keep all your items and char levels for next play though.
Which helps since the next game you are going to play you can do so lv 50+ dungeons early in the game to recruit more allies and get better items.
Also, some items are route specific. For example, at the end of Yuela's route you get a great sword in terms of stats called Disna.

I don't really care about items much and i had no plans on playing NG+ since the inflation of items and levels will ruin the game imo. Anyway, I still have a few questions. Will I have to fight against soldiers in Yela's route and how is Serawi's route?

The game balance seems fine to me.
You get a bunch of lv 50+ dungeons as new games. And you can also make all enemies stronger.

But anyway. In Yuela's route you will have to fight a bunch of Dysnafrody's soldiers in the last chapter (though, you don't "kill" them all). Also the war is only against Yuidora (or so it seems).
In Serawi's route you mostly fight demons and other monsters. The entire plot is "living together with other races" (which is basically "clear the pollution" a bunch of times) and monsters interfere with that. At the end of that route you will deal with the source of that problem.