Well the way to prune the blockchain is to store the merklehash only of all spent outputs if you can get a whole tree that has no spendable coins left. So if a bunch of old outputs all had their coins spent you can just prune that part of the tree and forget the blocks themselves and just store the merkleroot that represents the tree; but so many of the oldest coins are still unspent that there won't be a lot of benefit to this (I haven't done the analysis so this is somewhat a hypothesis).

You actually have it backwards, it's aproblem precisely because there are not transactions involving those addresses other than the initial block rewards; pruning the tree would make those coins unspendable, which would be unfair.

There are so many definitely-lost and likely-lost coins that I imagine at some point there will be a 'move your coins or lose them' mandate that will give people.. idk maybe 2 years or something to move coins to prove they aren't lost, and allow a large chunk of the blockchain to be pruned.