In your list of indexes, I saw some comments like "is this used directly?" and "this looks weird". I agree with you in that I can't imagine what uses those indexes, but I've also been surprisingly wrong about that before. Perhaps we could ask the DBAs to get us index usage statistics? @Jynus has gotten those for me before.
Topic on User talk:Brooke Vibber/Compacting the revision table round 2
... and I see that there's a "Revision indexes" thread below where uses of those indexes have already been identified :)