Alayavijnana is used to explain how karma is carried on from moment to moment, life to life, and also it is a basis for the continuation of a being. Here are some problems I have:
If alayavijnana is a part/mode of consciousness, why are we not aware of it?
If we can't be aware of it, what makes it part of the consciousness? / If there can be a part of consciousness one is not aware of, what makes it consciousness?
If only buddhas are aware of it, since they have it already purified, even they can't see the defiled seeds, and so it's only an assumption.
When we listen to someone speaking, it is the unconscious mind that is taking that sound and transforming it into recognizable speech. Doing that transformation is not a conscious activity. When we learn a new language, there is conscious effort for a while but in time the transformation becomes automatic with not conscious deliberation involved. The vast majority of information processing happens at the unconscious level with only some information percolating up to the conscious mind. One can legitimately ask, where is that transformation know-how stored? And why aren't we consciously aware of both the contents and functioning of our mundane unconscious mind? I'm not trying to be flippant, but that is just how we are constructed--it's a basic duality.
Now enter the notion of the alayavijnana. I haven't spent much time researching/reading about the alayavijana, but not too long ago I was reading Khenchen Thrangu's commentary on The Ocean of Definitive Meaning and came across this note that gave me pause,
There are two kinds of objects: objects that appear clearly and vividly to the six consciousnesses and objects that reside in the ground consciousness as latencies. When we perceive things in a room, there are also may other things outside the room that we cannot perceive. Where are they? They are in the ground consciousness, not as objects but as latencies. When we leave the room, then the room and the things inside it remain in our ground consciousness, since they are no longer appearing to any of the six consciousnesses.
The ground consciousness is vast in terms of the objects contained within it. The whole world is contained in the ground consciousness in the form of latencies. We can go anywhere in this world, and that place will appear, will become a vivid appearance, because everywhere we can go is already present as a latency in the ground consciousness. [KT] p.182