Haven't actually played amnesia though have looked into it's structure and setup. It definitely share's certain elements in common with this project esp. being of same type of genre.
I'm wondering if you couldn't do something with multiple monsters that could weaken you mentally or something. The larger monster will pursue you very inefficiently (this will end up being a factor of implementation, not ideas, in my opinion), but the other monsters will make you disoriented and slow you down, the effect becoming more pronounced each time you encounter and are unable to avoid them.
I like the use of multiple monsters combined with the actual singular larger monster but unfortunately have already used this particular mechanic in another place within the project. Though in that particular circumstance the smaller monsters did nothing more than watch/follow/surround you and over time that population level increased until such a point as the larger monster arrived.
I can see a similar mechanic being used inline with what you are thinking but am hesitant atm on it - nice thought though