Vanilla game has lots and lots of gameplay issues: skills not working as intended or not working at all, descriptions being wrong, decoctions not doing what they're supposed to do, quest levels and experience being weirdly distributed, etc.
The mod aims to create more challenging and balanced experience, while not deviating too far from vanilla system and principles, i.e. Ghost Mode is an overhaul mod which changes almost every aspect of gameplay: from combat and damage to loot and economy.