Well, I think you are needlessly mixing two things:
1) Long-term storage
2) Right-now usability
Neither of the formats is suitable for both of these goals - LRF is much more usable (for me: it is far more stable, has full justification, has fast intra-document links) while EPUB is a lot more future-proof (though not perfect).
Personally, I store all my books in (X)HTML (long-term storage) and convert them to LRF as needed (usability right now) using a single short command (I can get a book converted faster than the operating system recognizes a plugged-in reader).
It might be more difficult if you intend to buy books, but luckily that's not an issue for me - most of the stores don't sell to my country and those that do don't carry books I want.
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