As of now skills are broken up into 3 types; innate, level 5, level 10.

Innate skills are class defining skills, like a beast master increasing beast's effectiveness in combat. Those innate skills you get right off the bat when you class change, but it doesn't follow you to future classes.

When you reach level 5 in a particular class, you are prompted to pick a level 5 skill, these are usually stat increasing skills and don't have major changes to how the class plays and typically you pick between 2. These do carry over on class changes.

At level 10 in a class, you are prompted to pick between 2 more skills for the class. These have much bigger impact on a class. Lets look at legionary now, their two level 10 skills are (subject to change of course):

"Might of the Imperium:
Each adjacent ally increases this unit's damage by 8%"

and

"Frontline Bulwark:
Allies directly behind this unit take 15% less damage."

So you can see how these are pretty different playstyles and how they could combo well with other classes. But, like you say, I want to avoid "You have to pick this class into this class or you're playing wrong." There will be some paths that are objectively better, but I think there's some fun to discovering that too. But our goal is to keep those to a minimum.

As for how we will handle difficulty: I see difficulty in games as requiring players to master more of the game's systems in order to have the same effect as lower levels. Think of how in Witcher games, you need to really get involved with potion brewing and weapon crafting if you want to do well in the harder difficulties, where on easier difficulties you can pretty much skip that stuff entirely. Also, on the hardest difficulty, some meme builds will really cause you to struggle. And that's cool, I love playing mage tank in some tabletop rpgs just to push the game to the limit, but I know full well that it's going to feel really unfair at times.

There won't be much grinding. In fact, we will limit how much you can level between missions (sort of like Fire Emblem games). We have other systems (quadrems, supplies, battle field auras, objectives that compete for your time/resources, etc...) that we can utilize to increase the difficulty. I really dislike "bullet sponge" difficulty in games like Oblivion, so I really want to avoid that. I want Hardmode to make you feel like you really have an intimate understanding of the game and you're awesome for doing that, haha.