I actually made a theory on this before.
To me, Ghost Pokemon are in fact the spirits of deceased Pokemon, but through some Pokemon logic that I can't think of any way to explain right now, they are still a Pokemon after death. Just a different one. And the diverse appearances of Pokemon, such as
Banette,
Froslass, and Shandera, to name a few, might have connections as to how the Pokemon died. For example, Frolass might be a Pokemon who died of hypothermia, Shandera might be a Pokemon who was burned to death, etc. etc.
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