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The Underground was fucking awesome.
Digging for fossils, shards, and stones was some of the best fun I've had in a pokemon game. It was so strangely addicting, and it had real benefits and rewards to your work. The Secret Base element was a nifty adaption of what was originally introduced in Hoenn, and it was a phenomenal way to work in all of those items.
I was rather disappointed when it didn't return in B/W. Odds are it'll be forgotten from X/Y, too.