About Story mode, it should really be called a Hard Mode, as you should attempt it probably in the very end, after you get really good with the sandbox and figure out all the useful moves. It will punish you for every single mistake at some point. So, you have to consider basically every click you make, all the experience you gain, all the skills you learn.
About the main game, you're a bit mistaken. It's not a CRPG, it's rogue-lite, which means you will be losing. That's the way the genre works. For example, there are so called bonus points, which can make your life much easier, but you earn some of them by having Game Overs, and you get more of them when you play without saves, which means you are probably replaying them all over. And to know what skills will work you'll need experiments.
And in my opinion it works okay. Being defeated doesn't mean having a game over, it means getting an 18+ scene, so you're not wasting your time losing, you can kinda enjoy losing and getting used to the battle system.
Yeah, I agree that 90% of skills are worthless, and developers should consider taking out at least some of them, or making them like being extremely situational. But you absolutely can learn to make viable builds and defeat your opponents. You may check out wiki, Stats, Skills, Walkthrough pages, and anything else. Maybe it helps. Yes, the game has a pretty rough start, but that's what makes the adventure feel real for you. When you go around and pound their asses you know it's because you are better. And if you decide to go satisfy some enemies, you don't feel yourself a lazy whore. You could defeat them if you wanted, you just made a gift to them. That's much better than just having buttons to tap and mana to manage.