I think the biggest complaint I've seen so far is that there is too much random chance involved in the attacks (both to-hit and damage) - to the point that a battle that's going well for you can turn sideways in a hurry if you get bad RNG. But that's the whole point - this was made in an era where the strategy elements were made in a way to mimic tabletop strategy games that were also just completed based on dice. This is just digital dice. Modern gamers expect some sort of re-roll or rewind features maybe?
Another gripe I've seen is that there isn't some sort of auto-save between turns and you can only save between battles. Some of the battles can get pretty lengthy. But, the Switch has a standby mode that still works fine if you've got shit to do and want to put it away for a while and come back to it. Making autosaves between rounds would just lead to save-scumming (I guess that would give people their re-roll feature) which kind defeats the point. When you die in this game, you just go back to before the battle begins so you can reformulate your strategy. Modern strategy games like Triangle Strategy give you EXP even when you lose - which is cool, but would throw off the balance in this game that wasn't designed for that.
Lastly, I've seen people complain about the menu system here being "archaic". Which it kind of is, but also this is a pretty complicated game. You're not going to be able to achieve the same level of complexity by dumbing down the menus. Lots of modern games use pictograms and such to help with this, but this game doesn't have any of that. I'm personally pretty excited that they didn't fuck with the menus - because most of the time when that happens, they fuck it up.