Decay heat management, containing the residual radioactivity, and since 9/11 it should have been clear -- but evidently was not -- preventing the breach of the pit by a single missile or explosive. I would not call the pit a "secondary containment" area, given how easy it is to breach. Did all the air in that outer shell of a steel building at the Tepco plant go through filters, go was it open to atmosphere?
True, a pit at the top of vessel is needed during fuel cycling, but leaving much fuel for any length of time there is bad, and the reason -- the ENGINEERING reason, for good engineers learn from mistakes -- because when that pit is breached the whole of the plant -- the primary containment and the major plumbing, controls and power supplies are made very difficult to impossible to access.
In general on-site spent fuel has to be better secured.
It is not clear to me at this point if the Unit 4 SPF has been significantly damaged. There was some concern that there was fuel damage resulting from overheating when they lost the SPF cooling capabilities, or perhaps from debris falling onto the fuel from the damage to the roof and overhead crane when they had their hydrogen detonation. The pictures I've seen taken from above show a lot of debris and it is difficult to get a clear look. Until there is a close-up inspection it is all guesswork.