Okay, I've got to the end of current content, so here's my complete list of thoughts on the game so far. Before I start on the criticisms though, I'd like to say how incredibly interesting and varied this game manages to be, and how much I've enjoyed the journey so far. Even having beaten everything so far, I still don't feel like I'm even remotely good at the game, and that there are loads of strategies that nobody has even tried yet. Not to mention the meteoric pace of development. Plus it's refreshing to find a game where a hard encounter is beaten be playing smarter, instead of luckier or faster. Either way, here are all my collected thoughts so far. I'll put them in a spoiler tag since there's a lot of them.
Spoiler (click to show/hide):
(Apologies for the shitty formatting. List tags within spoiler tags doesn't appear to work, and I'd rather have the spoiler tag than the list)
The Thunderstorm rune is genuinely overpowered for most strategies, especially at lower levels. Level 1 is a strictly better flare, and equipping all of my females with Dark Runes makes most levels massively easier. I think the damage should be 1/2/3 in order to balance the rune rather than 2/3/4. Royal Way's difficulty could be maintained by simply using level 2 runes. The Eye would be made easier, but it wouldn't make much of a difference given that the main strategy for that level only involves taking 2-3 hits from them.
The difficulty is currently really spiky, with some levels being extremely tough, and some levels being almost trivial. The hardest levels (off the top of my head) are probably Royal Way and The Hand, and Photovol's recruitment mission, while most of the phasmos levels felt pretty trivial. I think one of the main issues is that in a strategy game like this, once you find a level particularly hard, you spend a while developing better strategies and building a better team, which means the levels post-spike become much easier, since you're now better at the game but the levels aren't as hard. This means that one extremely hard level can have a ripple effect on the difficulty of the whole game. Personally I really enjoy the super-hard levels, but the difficulty should be more consistent, whether that involves making the easier levels harder or the harder levels easier.
As others have mentioned, special attacks should have some kind of tooltip or descriptor telling you what they do. As it is, you just have to go by trial and error. That said, in later levels I just treat all specials as if they say "Kill all enemy units" - which some of them might as well do.
The Pecunia fight should have an option to skip the first 'cutscene' phase. Especially given that the third phase has an attack which instantly kills you without explaining what you've done wrong (which isn't that bad by itself), the player shouldn't be forced to repeat the long cutscene and trivial cutscene battle every attempt.
Vinara gets pretty tedious at 750HP. While Pecunia can get away with it since it's a very varied fight, Vinara only really has 1 (or 3 if you count diffierently), which just becomes a grind if stretched out too long. It would be a much more interesting fight at 500HP or less (possiblywith more damage dealt to compensate).
Somma is just... there are no words to describe that ridiculous difficulty. Without the stars aligning, absolutely flawless play, and a few miracles from several deities all on the same day, no mortal could possibly defeat this boss. Personally I'd reduce the damage of all her attacks tenfold at least, but something has to be done about this unbalanced monstrosity of a boss.
Photovol's current design feels somewhat unhealthy. She's utterly won me some fights (both of my successful attempts on The Hand have been from getting a lucky Photovol and just rushing units past the sleeping enemies), and is completely useless other times, entirely based on a coin flip. I'm a strong believer that "Roll a dice, if it lands on 6 you win" isn't healthy for a game. I'm not sure how you'd change it though, maybe just "Photovol puts enemies she attacks into a trance." - sounds overpowered but she's still weak to being counter-killed or just taken out via Flare/Thunderstorm.
Esurian solo animation lacks any text. I know it's a small thing, but all the others have some so it feels out of place.
The 10-1 ratio for converting runes and in the shop feels a bit off, especially since going up a tier only takes a few levels. 5-1 seems more reasonable for both. I've also mentioned elsewhere how the numbers on chanting feel a bit high. By the end of the game, I averaged only 25 of each unit type.
Not really a balance issue, but at some point I'd really like to see an Eva-Vs-An-Army mission. Her abilities look really interesting, especially in AoE situations, but so far we've almost never had more than one target to hit. On the topic of Eva-mode, some way to repeat bosses would be nice, since I'd like to try to beat all of the bosses with all of the classes (which also adds some replayability).
Anyway that's all I can think of for now. Once again though, these are tiny mostly QoL things in one of the best strategy games I've played in a long while, so thank you, either way.
Being able to see Eva during those animations would be a big plus. The four-star gorger animation is a perfect example; you can't see Beezelba at ALL, which is a damn shame. Watching her face while she has to hump a gorger into submission would be a treat. 
Also the four-star Mechiza animation. And the four-star hive animation... Hmm. There's a theme developing here.
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