For the non-psionic skills: for combat, not sure yet, I could still have skills that give bonus attacks depending on weapons type. For the non-combat ones, I'm thinking to go with Anima's suggestion: you have like 2-3 uses of each skill for each "chapter". It would guarantee 100% success rate. So in practice there could be each chapter 10 choices with the possibility to pass it with a skill check, but only 2-3 uses.
I think it's better than a random percentage like the first title since people would just rollback/reload anyway
Regarding the hit/miss it would be different. It would be either like QoT (a miss would still do half damage) or like Endless Legend game: there would be 4 sections of damage and percentages based on the stats. So could be like:
50% full hit = 10 dmg (base damage)
30% glancing blow = 5 dmg (half damage)
15% miss = 2 dmg (1/5 of base damage)
5% critical hit= 15 dmg (+50% base damage)
even a miss would still deal 2 dmg. So imagine a machinegun with very low accuracy, but a good rate of fire, could fire 5 bullets and even do all "misses", would still be 10 dmg. And instead a sniper rifle with a base attack of 10 even with a critical could do 15 dmg. So in the end only 5 dmg of difference. (that's an extreme case example).
Done like this it could be interesting and "fun" even when missing I think, since you'd need to take into consideration other aspects like ammo remaining and maybe if Anima can implement this, the time consumed for each attack: it would be either a point system like Fallout games or a "real" timer for each attack, so with a fast weapon you could fire twice in same amount of time you fire once with a slower one, etc.
In practice need to learn to design the games in a "smarter" way, so that I don't have to spend 4 months doing 100 skills, when you can still have fun with 20 skills but better designed