So, what happens when Bitcoin takes over the world economy, and 54 uBTC is worth a lot of money ($54 say)? Then Bitcoin will only be usable for large-value transactions... It will be more like the existing inter-bank wire-transfer system at that point...
Then you just adjust the threshold down. The behavior isn't a protocol rule, miners can still include transactions with smaller outputs. The whole idea is just to prevent floods of transaction outputs which are uneconomical to redeem (e.g. costs more to redeem than the value of the txout returned), and to increase the cost of abusing the blockchain for data storage in that way.