Any idea how to fix it without blocking the player's progress or making the mechanics mostly irritating (and really not limiting)? The system would also have to be understandable to the player. Practically, the only idea that could effectively limit the rest are time limits, but if larian introduced it, players would pull out forks and torches (this will not pass in such a large game). We are discussing ideas and still have not been able to find a reasonable compromise.
Resting worked great in BG1 & 2. No need to reinvent the wheel. Just use the constraints and limitations the series has already been using.
